Meshmixer for Dental Models: Trim a Scan and Add a Base

An intraoral scan exported as STL is rarely ready for the printer. It is an open surface with a ragged edge where the scan stopped, a few small holes, and no base to stand on. Autodesk Meshmixer can fix all three in a few minutes, and it is free.

The short answer: import the arch, trim the ragged edge with Edit > Plane Cut or the brush selection, select everything, run Select > Modify > Smooth Boundary, then Select > Edit > Extrude with EndType set to Flat to build the base. Close leftover holes with Analysis > Inspector and export as binary STL. This is the sequence Formlabs documents for turning intraoral scans into models, and the settings below come from Autodesk’s own Meshmixer help.

One thing to know first: Meshmixer 3.5 (2018) is the final release. Autodesk still lists it as free for Windows 64-bit, but states it is no longer developed or supported. It has no dental module, no model base templates and no tooth library; everything here uses its general mesh tools.

What you need

Step 1: Import the scan and check its size

Use File > Import and open the arch STL. Before cutting anything, open Analysis > Units/Dimensions. It draws a bounding box and shows the X, Y and Z size of the model. A full adult arch should read in tens of millimetres; if the numbers look a factor of ten or a thousand off, the file was imported with the wrong unit assumption.

To correct it, type the right value for one dimension (the object scales uniformly) or use Set From Measurements on a feature of known length. Fix the scale now; every later offset depends on it.

Formlabs suggests orienting the view with the anterior teeth at the top and the unrefined edge on one side, which makes the plane cut easier to place.

Step 2: Trim the ragged scan edge

You have two options, and most people use both.

Plane Cut for straight trims

Choose Edit > Plane Cut. A transform gizmo appears; click and drag to draw a line along the edge you want to remove. The side that will be discarded is shown transparent. If the wrong side is transparent, click the blue arrow to flip the cutting direction, then Accept.

Plane Cut also has a Cut Type and a Fill Type. When a cut crosses a closed solid, Meshmixer fills the opening with a planar patch by default, so cutting a solid gives a solid. Fill Type offers No Fill, Minimal Fill, Remeshed Fill and Fixed Fill. On an open intraoral scan the cut simply removes the unwanted strip; the base comes later.

Brush selection for irregular areas

For tags of soft tissue, a tongue or cheek artefact, or a wavy vestibular edge, use the Select tool with the brush. Paint over the area (it turns orange) and press Delete. Repeat for each spot. Take off a little at a time so you do not remove gingival anatomy you need.

Step 3: Smooth the boundary

Select the whole mesh with Ctrl+A (Command+A on a Mac build, if you still have one). From the selection menu choose Select > Modify > Smooth Boundary and Accept. This evens out the saw-tooth outline left by the scanner and the trimming, so the base wall you extrude next has a clean edge instead of spikes.

Step 4: Add the base with Extrude

With the whole mesh still selected, choose Select > Edit > Extrude (hotkey D). Autodesk describes the tool as disconnecting the selection along its boundary, moving it, and stitching the two boundaries together with a tube of triangles. For a model, that tube becomes the base wall.

The settings that matter:

• EndType: Flat. The default, Offset, just copies the scan surface. Flat projects the end onto a plane perpendicular to the extrude direction, which gives the model a flat bottom that sits on the build platform.
• Direction. The default, Constant, moves every vertex along the average normal of the selection. You can also extrude along the world X, Y or Z axis, which is useful when the occlusal plane is already aligned to an axis. Flat is not available in Normal mode, where each vertex moves along its own normal.
• Offset. Sets how far the base extends from the scan. Drag the sphere handle or type a value; Formlabs notes that a negative value may be needed depending on which way the model faces. Watch the preview and stop when the base reaches the height your lab uses.
• Harden and Density. Harden adds a narrow ring of triangles at the boundary for a sharper edge; Density adds subdivisions along the extrusion. Both can usually stay at their defaults.

Accept, then check the base from below. If the wall has gaps where the scan edge was very uneven, undo, smooth or trim again and re-extrude.

Step 5: Close holes and check the mesh

Open Analysis > Inspector. According to Autodesk’s help, it marks three kinds of problems with coloured pins:

• blue – holes in the mesh;
• red – non-manifold regions (edges shared by more than two triangles, “bowtie” vertices);
• magenta – small disconnected pieces, which repair simply deletes.

Click an individual pin to fix that spot, or use Auto Repair All to repair each issue in turn. Holes can be filled with Minimal Fill, Flat Fill or Smooth Fill; Smooth Fill follows the surrounding curvature and usually suits small gaps in tooth or gingiva surfaces. The Small Thresh value decides what counts as a small component, so check that it is not set high enough to remove a separate piece you want to keep.

If the Inspector cannot close the model cleanly, Edit > Make Solid rebuilds the object as a watertight solid through a voxel representation. It can soften fine detail, so compare the result with the original before you rely on it.

Step 6: Export for the printer

Use File > Export and choose STL Binary, which is the format Formlabs specifies for the result. Save it under a new name so the untouched scan stays available. Hollowing to save resin (Edit > Hollow) is a separate step, done after the base is in place.

Limitations

• No dental tools. Meshmixer has no model base templates, no die or margin tools, no tooth library and no articulator. A base built with Extrude is a plain extrusion, not a lab-standard base with articulator mounting.
• Discontinued. No bug fixes or support from Autodesk. Very large scans can make it slow or unstable, so save often and reduce heavy meshes first.
• Not a medical device. Meshmixer is not validated for clinical measurements or appliance design; use it for model preparation.
• Windows only in its current official form.

If these limits matter for your lab, our comparison of maintained Meshmixer alternatives for dental STL work covers free tools that are still developed, and the free 3D mesh and scanning software hub lists the rest. If the model starts from CBCT rather than an intraoral scan, create the surface in 3DimViewer first and use Meshmixer only for the clean-up. For capturing a physical cast with a depth sensor, Skanect (shareware, conditionally free, being phased out) produces STL files that go through the same steps.

FAQ

Can I use Meshmixer for dental models?

Yes, for model preparation: trimming intraoral scans, adding a flat base, filling holes, hollowing and exporting STL for printing. It has no dental-specific functions and is not validated for clinical design work.

Is there a Meshmixer dental download or dental edition?

No. Autodesk only released one general Meshmixer, and the final version is 3.5 for Windows 64-bit. Sites offering a “Meshmixer dental” edition are not Autodesk.

Is there a dental library for Meshmixer?

Autodesk does not provide a tooth or model base library for Meshmixer. Bases are built with Extrude, as described above.

How do I fill holes in a dental scan in Meshmixer?

Open Analysis > Inspector, then click the blue pins or use Auto Repair All. Choose Smooth Fill for small gaps on curved surfaces. Leave the large opening at the scan edge alone until the base is extruded.

How do I cut part of a model in Meshmixer?

Use Edit > Plane Cut for straight cuts (the blue arrow sets which side is removed) or the Select brush followed by Delete for irregular areas.

Last updated: 29 September 2026 · DentSoftPro editorial team. Licence, version and platform details are checked against each developer's official documentation; none of the tools listed here should be treated as a certified medical device unless its vendor says so.