Our 10 steps to creating 3D printed anatomical models

3D printed cat skull in hand
Transform your teaching, get new insights into your research, and add that “Wow!” factor to your outreach with your own 3D physical model.

If you’ve ever tried buying clothes online, you’ve experienced the great challenge of understanding a physical object through a virtual interface and photographs. Yes, you can get a basic grasp of the color and pattern or design but the feel of the fabric, the fit on your body, the look from the front versus the side or back, how it conforms to your movements; these fundamental properties of clothes are impossible to understand virtually. Yet, once you have that item of clothing physically in hand, you would see and feel these properties the instant you try it on. That is the power of learning through physical interaction.

What is true for clothing is even more true for learning or researching anatomy, where there are parts with unfamiliar and complex geometries, lengthy lists of terms, and numerous interactions among parts. Unlike virtual models, which engage only your visual sense, you can handle and manipulate physical anatomical models to engage your visual and tactile senses simultaneously; not only do you learn better with “multisensory” (vs. unisensory) learning, you’re more likely to remember what you learn (Shams & Seitz, 2008; Ekwueme et al., 2015). It’s also easier to test physical interactions with physical models, such as how two bones articulate, how fluid flows across or around a structure, or the consequence of different moment arms for leverage. And orientation and scaling become more intuitive once you can orient a physical model relative to other models or your own body.

Photo of a 3D printed bird femur and tibia being articulated by a pair of hands
With physical models, you’ll find it much easier to explain scale, orientation, and how structures interact physically with each other and the environment.

While specimens have traditionally been used to provide this physical modality in anatomy (and there are many benefits of specimen-based learning!), physical models have advantages over specimens, especially when used as a complement to specimens and virtual models. Dissection specimens are typically used just once and then thrown away, whereas models can be used repeatedly. Rare specimens that are damaged through repeated use cannot be easily replaced, whereas models can. Specimens that are too small (e.g., middle ear bones) or too large (e.g., elephant skull) to be handled can be scaled to the appropriate size for handling as a model. And soft tissues, that would otherwise be difficult to preserve for long-term use, can be recreated as a durable model.

Photo of 3D printed dogfish shark denticle (scale) at 100 times life-size scaling held in a hand
For a human to interact effectively with an object, that object must be at human scale. If your structure of interest is very small or very large, we can create a physical model scaled to a size appropriate for handling. For example, this dogfish shark scale, printed at 100X life-size, would otherwise be invisible to the naked eye.

These are all the reasons we love helping people turn their digital data (whether mesh files, medical imaging data, confocal stacks, or photographs) into physical models that will transform their teaching, give them new insights into their research, and add that “Wow!” factor to their science outreach. In this blog post, we walk you through the steps we take in creating physical models so that you know the attention to detail and quality you’ll receive in working with us. Even though we specialize in anatomical models, we’re also happy to work on non-anatomy models too! Once you’re ready to bring your digital data to physical life, contact us to get started!

We can print your digital mesh models at extremely high resolution. For example, a client asked us to create a model of this alligator femur with the surface roughness in the original mesh. Can you tell which of these is a digital rendering of the mesh model and which is the physical 3D print? The digital rendering is on the left and the 3D print is on the right. (Shared with the client’s permission)

1. Understand your needs

Our first step in creating a physical model is to understand your needs and intended uses for your model. This can begin with you sending us some basic details through our 3D printing service contact form. If all you need is a 3D print of a mesh file (i.e., an OBJ, STL or PLY file with vertices, edges, and faces), we can follow up directly with a quote after we make sure we get the proper scaling.

For more complex projects, it may be necessary for us to follow up with a meeting to hear more about your needs, ask questions, and offer recommendations. For example, if you need to show how multiple structures connect or articulate with one another (e.g., bones of the skull, components of a protein complex), we might recommend 3D prints of each element in a different color with embedded magnets so that the pieces can be easily attached and detached. Or if you need to demonstrate how structures move relative to one another (e.g., a knee joint), we would recommend a multi-body physical model with 3D printed rigid elements joined together with artificial ligaments (e.g., woven polyester) or molded silicone pieces. As expert biologists and anatomists, we “speak anatomy”; this greatly facilitates communication about how to approach particular anatomical features, such as bilateral asymmetry, distinctions between tissue types, etc.

Photo of 3D printed shark braincase with left and right halves held by hand slightly apart
If your model has internal and external geometry, we can “cut it in half” and add magnets so that you can easily demonstrate both aspects with the same model. For example, we printed this dogfish shark braincase as left and right halves with embedded magnets to easily snap apart or together (2X scaling).

Starting with an in-depth understanding of what you need and how the model will be used ensures that we create a model uniquely tailored to you.

2. Create a quote

Once we understand the full scope of the project, we generate a quote with all the details of the order (e.g., number of prints, number of copies, color, scaling, materials, delivery date, cost) and send this to you for your review. Through the quote, you can make sure we’ve understood exactly what you want and get a clear commitment on cost and delivery. Once we receive payment or a purchase order for the quote, we begin creating the model!

Photo of a 3D printed cat cranium in lateral and ventral view
If you have a digital mesh of a skull, we can print it at high resolution. For example, on this cat skull model, created from a micro-CT scan and printed at 1.25X scaling and 0.1 mm resolution, you can see nearly all of the suture lines. Top is lateral view; bottom is ventral view.

3. Prepare a digital version of the model

The first step to creating the model is preparing a digital version of the model for 3D printing or molding. If you already have mesh data, such as an OBJ or STL file, that you want printed, we can skip this step.

Digital rendering of a cat cranium with the bones in different colors
The first step in creating your model is preparing a digital version of the model, such as this digital cat cranium. If you already have a digital version of the model, we can use that one directly.

However, in another case you may have 3D imaging data (a CT scan, an MRI scan, confocal microscopy data), from which you would like to create a 3D model. As anatomists with expertise in medical imaging, we can identify and separate the target structures from these data (called “segmentation”) and export the structures as meshes.

Screenshot from the medical imaging segmentation software 3D slicer with a micro CT scan of a cat skull loaded
If you don’t have a digital model yet, we’re happy to create a model for you by segmenting medical imaging data like CT or MRI scans, as shown here for a micro-CT scan of a cat skull.

Creating a 3D model doesn’t always require the original data to be three-dimensional. If you don’t have mesh files or 3D imaging data, we can sometimes create 3D models from a series of photographs or even illustrations. If you don’t need a model that matches a particular specimen precisely, a 3D model created from several photographs (e.g., taken from all axial views) is usually within the structure’s natural range of variation. This can be perfect for models that are intended to be conceptual rather than represent a particular specimen.

A series of photos of a dogfish shark tooth viewed under a dissection scope and a photo of a 3D printed dogfish shark tooth model held in a hand
If you don’t have 3D data, we may still be able to make you a 3D model! We can use a series of photos taken from different angles to sculpt a 3D model, such as this shark tooth model (bottom right) that we created based on dissection scope photos from at least five different views.

The final step of creating a digital version of the model is removing any artifacts, if requested. For example, the surface of meshes created from medical imaging may have an artificially roughened or bumpy surface as a result of the scanning or segmentation process. Another example is the deformation of a specimen as a result of preservation and storage (e.g., fish fins and bodies bent from being fixed and stored in jars). If you wish, we can digitally correct these artifacts so that the physical model better reflects the natural anatomy, not the scanning or preservation method.

Digital rendering of two alligator femurs, one with a noisy surface texture and the other with a smooth surface texture
If your data has artifacts such as surface roughness not naturally occurring in the specimen (left), we can remove this for you before printing (right). (Mesh models of alligator femur rendered in Blender)

4. Modify the digital model for 3D printing or molding

Once we’ve prepared and cleaned up a digital version of the model, we may need to make modifications to allow it to be 3D printed properly. For example, if the model is too large to be printed or molded as a single unit, we can break up the model into several smaller pieces. Printing long, thin structures attached to larger objects can also be problematic because the thin portions are easily broken when removing the support structures from the completed 3D print. In this case, we can digitally separate the delicate portions of a model, print them separately, and attach them after removing the support structures.

Photo of a 3D printed loon pelvis with telescoping highlight boxes showing tongue and groove joints created in a digital model at a joint between the pubic bone and rest of the pelvis
If your model has fragile elements, we will figure out the best way to both print and strengthen those elements in the final model. For example, when creating this loon pelvis model (left), we digitally separated the pubic bones (top right square) to print them separately and then created multiple tongue-and-groove joints (one shown in bottom right square) to attach them securely to the rest of the pelvis after printing.

A common problem when 3D printing meshes created from medical imaging data is that if the wall of a structure is too thin, the wall will either have holes or disappear entirely when 3D printed. This is because when the mesh is converted into a file for 3D printing (a process called “slicing”), any portions of walls with a thickness less than a particular threshold are treated as if there were no wall. By inspecting the “sliced” model, we can identify any problem areas and digitally increase the thickness of those areas so that they are printed at the thinnest width allowed by the 3D printer (approximately 1 mm).

Screenshot from Blender showing the wall thickness of a cat cranium mesh model through heat map color coding
Before printing, we make sure that all the “walls” of your model are thick enough for 3D printing and we correct any thin spots. This ensures that your model doesn’t have unintended holes or “translucent windows.”

5. Modify the digital model for additional materials

The next step is modifying the digital model to include any additional materials you want in the physical model. For example, if we’re adding magnets to the model, we add holes in the digital model so that after it’s printed we have perfectly sized holes for inserting the magnets.

Screenshot from Blender with telescoping highlight box showing a compartment created in a mesh model with a magnet inside the compartment
To add additional materials to your model, we create compartments or attachment points in the digital model so that we can easily insert or attach materials after printing. For example, to add magnets to this shark braincase model, we created compartments in each half and inserted the magnets after printing.

This allows for pieces of the model to be easily attached and detached so that you can easily show the inside and outside of a model or how elements articulate with one another.

Photo of two 3D printed shark braincases, one with the left and right halves held just barely apart and one with the left and right halves joined together
Magnets are perfect for models that are “cut” into separate parts, such as these left and right halves of a dogfish shark braincase. This allows you to quickly show the internal anatomy of a structure or snap the parts together to show the outside.

We can also add other shapes to the digital model, such as hooks or pegs, for attaching other materials such as artificial ligaments or molded silicone components.

6. Slice the model

Now that the digital model is ready to be 3D printed, we convert it into a format the 3D printer can “understand” through a process called “slicing.” Since 3D printing builds a 3D object by laying down one layer at a time, this process “slices” a 3D shape into each of these sequential layers. Since a 3D printer must also always print onto something (it can’t print on thin air), slicing also adds support structures so that every part of the 3D printed structure has something underneath it.

One of the goals in slicing a model is to minimize the number of supports needed; the more supports that are needed, the more time it takes to remove and clean the finished print. Another consideration is making sure the supports are attached to the most robust parts of the model; this reduces the chance that the model will be damaged when removing the supports. We test various orientations of the model to find an optimal orientation.

Screenshots from PrusaSlicer of a cat cranium on a 3D printer bed in four different orientations and four corresponding different support arrangements
We’ll determine the best orientation of your model (orange) for printing so that any supports (green) can be removed without damaging any delicate structures and so that surface artifacts are minimized.

As mentioned previously, a 3D printer works by depositing hundreds, or even thousands, of individual layers on top of each other. The height of those layers determines the resolution of the model in the vertical dimension: the shorter the layer height, the higher the resolution. However, shorter layer heights also increase the total time required for printing because of the greater number of layers.

After we’ve determined the optimal orientation for the print, we set the layer height depending on the resolution that you want. If you don’t need the highest resolution, we can decrease the cost of the print by using wider and fewer layers. The slicing software allows us to even set different layer heights for different regions of the print. We love this feature because it allows us to increase the resolution in flat regions (where layer lines are more obvious) and decrease the resolution in vertical regions to lower the overall print time and cost of your model.

7. Print the model

At this point, we’re ready to 3D print the model! It can take 15 minutes or more than a day to 3D print a model, depending on the size and resolution. While our printers don’t require constant monitoring (can you imagine?!), we do check on them throughout the printing process to ensure everything is printing properly and replace the filament if the printer runs out mid-print. For projects where pieces must snap or fit together, we may print a series of prototypes to test which dimensions give the intended functionality.

Photo of an Original Prusa MINI 3D printer printing a long bone
One of our 3D printers (Original Prusa MINI) in action!

8. Clean and post-process the 3D prints

As mentioned previously, any overhanging structures on a model require “supports.” So once a part has finished printing, we remove any of those support structures. This must be done manually but we’ve developed techniques and tools to do this quickly. The time to remove the supports depends on the size and geometry of the model and can take anywhere from a few seconds to up to 15 minutes.

Photo of a 3D printed cat cranium with supports and with supports removed
After printing, we’ll remove any supports from your model (left) to reveal the final print (right).

Sometimes, the printing process leaves thin strands of plastic on the printed part, called “stringing”; this is a natural part of the printing process when using plastic filament. We use a heat gun to quickly blast away these thin strands.

Photo of a heat gun blowing on a 3D printed cat mandible with thin strings of plastic attached
If your model has any stringing (a natural part of the printing process), we’ll remove it using brief passes of a heat gun.

The printing process can also leave surface artifacts, such as poorly adhered layers and uneven areas where support structures were attached. If present, we remove these artifacts as best as possible using a grinding tool.

Photo of a Dremel tool with a 952 grinding stone attachment used to clean the surface of a 3D printed cat cranium
We’ll also remove any large surface artifacts from the printing process, using a rotary drill fitted with a grinding tool. For the cat cranium model, we used a Dremel® with the 952 grinding stone attachment.

3D prints created using the filament extrusion process have visible layer lines, although these are generally less than 0.20 mm thick. If you would rather have a finished surface, where the layer lines are not visible, we can sometimes offer this, depending on the size and complexity of the model. To remove the layer lines, we manually grind and sand the surface, giving it the feel of terracotta or unglazed clay.

Photos of a 3D printed dogfish shark tooth with an unfinished or raw surface where layer lines are visible and a smoothed terra cotta-like surface
If you opt for the basic surface quality, your print will have visible layer lines (left). However, they are not easily discernible for high resolution prints, where the layer lines are less than 0.1 mm thick. Depending on the size and complexity of your model, we also offer a finished surface (right), where we remove most or all layer lines by manually grinding and sanding the surface.

9. Combine parts and add additional materials

For the final step of creating a model, we glue together any parts that we printed separately. We also add any additional materials to the 3D printed parts, such as artificial ligaments, silicone-molded components, or magnets. If we’re adding magnets, we insert these into the compartments that we added to the digital model (ensuring the proper orientation!) and fill and cap the compartment with clear melted plastic so that the magnet doesn’t come out.

Photo of a plastic heat gun injecting melted plastic into a magnet compartment along the edge of a 3D printed shark braincase
If your model includes magnets, we’ll inject plastic around and over the compartment holding the magnet so that the magnet stays in place.

10. Pack and ship the model

Once we’ve completed your model, we carefully pack it up (using 100% renewable and recyclable materials) and ship it to you!

Photo of 6 3D printed cat crania packed in a tab-locking cardboard box for shipping
Once your models are done, we’ll pack and ship them to you!

We hope that this post has sparked some ideas on how you can incorporate physical models into your work, research, or teaching. We also hope it has given you an idea of the care and expertise you will receive in working with us. Are you ready to wow your students, impress your colleagues, and gain a new perspective through hands-on, multisensory interaction? If so, start by contacting us. We look forward to hearing from you!

Have a question or comment? Please leave it below!

Written by Aaron Olsen

Edited by Naomi Robson

Images and photographs by Aaron Olsen

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