Meshlab

Cleaning 3D Meshes

By Alejandro Romero

Cleaning 3D Meshes in MeshLab

Total time: ~15 min

The primary use case for MeshLab is cleaning up 3D meshes in a comprehensive environment. Though many 3D modeling software include such features, MeshLab has a more extensive and fleshed-out mesh decimation pipeline allowing for more control over mesh cleaning. One workflow is outlined below.

Open MeshLab and load in the mesh: File → Import Mesh → [Select your mesh]
To clean up your mesh, apply tools in Edit or Filters. Some very useful filters include:
- Filters → Cleaning and Repairing → Remove Isolated (wrt Diameter)
  - Adjust the max diameter percentage until artifacts are removed.
  - Clean any undesired artifacts smaller than the desired final mesh.

- Filters → Remeshing, Simplification and Reconstruction → Simplification: Quadric Edge Collapse Decimation
  - Reduce the vertex count of the mesh for reduced file size.
  - Adjust the Percentage reduction parameter to simplify the mesh. Because this is a percentage, it’s helpful to begin with a larger value to be preserved (e.g. 0.8) and work down from there. The current vertex count can be viewed in the bottom right (purple window).
  - Click Apply to simplify the mesh accordingly.

3. To save the final mesh:

- File → Export Mesh As
- Select .obj at the bottom of the popup menu and select your desired directory.

4. If your mesh contains unconnected parts that you want to export separately:

Make sure the Layer Dialog is toggled on and find your mesh (there should only be one for now).
Right-click on the mesh name and click Split in Connected Components in the drop-down.
IMPORTANT: If your 3D Slicer OBJ contains a lot of artifacts (they usually do), make sure you followed step 2a. properly. If not, all artifacts will be separated into individual meshes, which may crash the program.
Select each separated piece of the mesh and export them individually as described above.

5. Congratulations, you now have a clean, segmented mesh!