Fill Holes

The Fill Holes tool automatically detects and fills holes (open boundaries) in surface meshes, creating watertight geometry suitable for 3D printing, simulation, and other applications that require closed surfaces.

Medical Disclaimer

This tool is provided for research and educational purposes only. Any clinical or diagnostic use requires proper validation in accordance with applicable regulations.

Overview

Holes in surface meshes are open boundaries where edges are connected to only one triangle instead of two. Holes commonly occur from:

• Cutting or clipping operations
• Mesh editing that removes triangles
• Incomplete segmentation
• Import of non-watertight geometry

The Fill Holes tool provides two modes of operation:

• Fill all holes: Automatically fill all holes up to a maximum size
• Identify holes: Display hole statistics and selectively fill specific holes

Interface

Fill All Holes Mode

When this mode is enabled, all holes within the specified size limit are filled automatically.

Parameter	Description	Default
Maximum hole size (mm)	Only fill holes with diameter ≤ this value	10.0

This threshold prevents accidentally filling large openings that should remain open (such as pipe ends or intentional openings).

Identify Holes Mode

When this mode is enabled, holes are detected and displayed in a statistics table:

Column	Description
ID	Unique identifier for the hole
Diameter (mm)	Approximate diameter of the hole
Edges	Number of boundary edges forming the hole
Selected	Checkbox to mark holes for filling

Holes are highlighted in the 3D view for visual identification. Select specific holes in the table to fill only those.

Actions

Button	Description
Apply	Fill the specified holes

Hole Filling Algorithms

The Fill Holes tool uses algorithms optimized for different hole shapes:

Simple Holes

Small, roughly circular holes are filled with a minimal number of triangles, creating a planar or slightly curved cap.

Complex Holes

Larger or irregularly shaped holes are filled using algorithms that:

• Respect the local surface curvature
• Create well-shaped triangles (good aspect ratios)
• Blend smoothly with the surrounding surface

Typical Workflows

Fill All Holes Automatically

For surfaces with many small holes:

1. Open the Fill Holes tool
2. Enable Fill all holes mode
3. Set an appropriate Maximum hole size
4. Click Apply

All holes smaller than the threshold are filled.

Selective Hole Filling

To fill only specific holes:

1. Open the Fill Holes tool
2. Enable Identify holes mode
3. Review the table of detected holes
4. Click on holes in the 3D view or table to select them
5. Check the Selected column for holes you want to fill
6. Click Apply

Only the selected holes are filled.

Preparing for 3D Printing

To ensure a surface is watertight:

1. Run Diagnostics and Fixes to identify all issues
2. Open Fill Holes and identify all holes
3. Review hole sizes—very large holes may indicate intentional openings
4. Set Maximum hole size appropriately
5. Fill holes
6. Re-run diagnostics to verify the surface is closed

After Cutting/Clipping

After using Cut or Clip tools:

1. Open Fill Holes
2. Enable Identify holes to see the new openings
3. Fill holes as needed
4. Note: For clean planar caps, use Clip with Closed clip option instead

Best Practices

1. Use Identify mode first: Before filling all holes automatically, use Identify mode to understand what openings exist and their sizes.

2. Set appropriate thresholds: Use the Maximum hole size parameter to avoid filling intentional openings like pipe ends or cavity entrances.

3. Check the results: After filling, verify that:

   • Filled regions have appropriate geometry
   • No unintended openings were filled
   • Surface remains manifold

4. Consider alternatives: For planar cuts, using Clip with Closed clip creates cleaner caps than hole filling.

5. Run diagnostics after: Use Diagnostics and Fixes to verify the surface is now closed and manifold.

6. Smooth if needed: Large filled regions may benefit from Smooth to blend better with surrounding geometry.

Hole Size Considerations

The hole diameter is calculated as the diameter of a circle with equivalent perimeter length. This is an approximation—irregular holes may be larger or smaller than their calculated diameter suggests.

Hole Size	Typical Source	Recommendation
< 1 mm	Mesh artifacts, numerical precision issues	Fill automatically
1-10 mm	Small defects, editing artifacts	Review and fill
10-50 mm	Cutting operations, significant defects	Evaluate carefully
> 50 mm	Intentional openings, major cuts	Usually leave open or use Clip

Troubleshooting

Holes Not Detected

If holes aren't appearing in the table:

• Ensure the surface has actual open boundaries
• Check that you've selected the correct surface
• Run Diagnostics and Fixes to verify hole count

Poor Fill Quality

If filled regions look incorrect:

• Large, complex holes may not fill well—consider using Voxel Remesh instead
• Very elongated holes may need manual triangle editing with Editor
• Apply Smooth to improve the transition

Too Many Holes to Fill Individually

If there are many small holes:

• Use Fill all holes mode with an appropriate maximum size
• Consider using Voxel Remesh which closes holes during processing
• Check if the source data or segmentation can be improved

See Also

• Diagnostics and Fixes - Comprehensive hole detection and mesh repair
• Clip - Create clean planar cuts with caps
• Cut - Remove portions of surfaces
• Editor - Manual triangle editing for complex holes
• Voxel Remesh - Alternative approach that closes holes during remeshing