Clip

The Clip tool trims surfaces using clipping planes and other geometric tools, with the option to create closed (capped) surfaces at the clip boundary. This is particularly useful for creating cross-sectional views, preparing surfaces for 3D printing, or trimming surfaces at precise locations.

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

Clipping provides a clean, geometrically precise cut through surfaces, using a plane, cuboid, sphere or cylinder as the clipping region. Unlike the Cut tool, which follows the mesh of an arbitrary ROI shape, the Clip tool cuts against the exact analytic region—which is what allows the plane and cuboid regions to keep the result watertight with a properly capped boundary.

The tool offers various region orientations and interactive positioning, making it easy to clip surfaces at any angle or location.

Interface

Clipping Region

Choose the region shape, then position it using interactive handles in the 3D view. The region can be translated, rotated, and resized.

Region	Description
Plane	An infinite plane, alignable to the orthogonal planes (XY, YZ, XZ)
Cuboid	A box defined by its six faces
Sphere	A sphere defined by its center and radius
Cylinder	An infinite cylinder along its axis; the cylinder is not capped

Pointer Controls

When a clipping region is active, use the following controls in the 3D view:

Region	Interaction
Cuboid	Left-drag a face or handle to adjust it. Ctrl+left-drag translates the cuboid, and Ctrl+right-drag resizes it.
Sphere	Ctrl+left-drag translates the sphere. Ctrl+right-drag resizes it.
Cylinder	Ctrl+left-drag a part of the widget to adjust the cylinder. Ctrl+right-drag resizes it.
Plane	Ctrl+left-drag a part of the widget to adjust the plane. Ctrl+right-drag resizes it.

These controls take precedence over 3D view navigation while the pointer is over the clipping region.

Clip Options

Option	Description	Default
Closed clip	Create a cap over the clipped region, closing the surface	Disabled
Invert	Clip the outside region instead of the inside region	Disabled
Retain clipped region	Save the removed portion as a new surface object	Disabled

Options a region does not support are hidden:

Region	Closed clip	Invert	Retain clipped region
Plane	✓	✓	When Closed clip is off
Cuboid	✓	When Closed clip is off	When Closed clip is off
Sphere		✓
Cylinder		✓

Closed cuboid clipping always keeps what is inside the box, so it has no side left to invert and no removed portion to retain.

Parameters

Closed Clip

When enabled, a new triangulated surface is created to cap the cut boundary, resulting in a watertight surface. This is essential for:

• 3D printing preparation
• Volume calculations
• Boolean operations

Requirements

The Closed clip option requires the input surfaces to be closed and manifold. Surfaces that are not closed and manifold are reported and left unchanged, and the operation continues with the remaining surfaces. To find and repair the boundary and non-manifold edges that keep a surface open, use Diagnostics and Fixes.

Meshes generated from a multi-label mask preview are a common case: they often carry boundary or non-manifold edges and therefore have to be repaired before closed clipping can run.

Invert

Controls which side of the clipping plane is removed:

• Unchecked: Remove the portion on the default side (typically inside/below)
• Checked: Remove the opposite portion (typically outside/above)

The preview in the 3D view updates to show which portion will be retained.

Retain Clipped Region

When enabled, the removed portion is not discarded but instead saved as a new surface object. This effectively splits the surface into two parts along the clipping plane.

Actions

Button	Description
Reset	Reset the clipping region to the bounding box center of selected surfaces
Apply	Execute the clipping operation

Empty results

A clipping region that would remove the whole mesh of a surface leaves that surface unchanged and reports it, so a badly placed region never empties a surface. Move, resize or invert the region, and then apply again.

Clip vs. Cut

Feature	Clip	Cut
Planar cuts	✓	Limited
Freehand shapes		✓
Analytic regions (plane, cuboid, sphere, cylinder)	✓
Arbitrary primitive ROI meshes		✓
Closed (capped) surfaces	✓
Interactive region positioning	✓	✓
Best for cross-sections	✓
Best for irregular regions		✓

Scripting

The same operations are available from the scripting API, using a primitive object as the region:

import ScriptingApi as api

app = api.Application()
surface_operations = app.get_surface_operations()
primitive_operations = app.get_primitive_operations()

plane_roi = primitive_operations.create_plane([0, 0, 0], 100.0, 100.0, "ClipPlane")

# surfaceNames, primitiveName, closed, invert, retainClippedRegion
surface_operations.clip_with_primitive(["MySurface"], plane_roi, True, False, False)

See clip_with_primitive() and cut_with_primitives() in the Surface Operations API reference.

Typical Workflows

Creating a Cross-Section

To create a clean cross-sectional cut:

1. Open the Clip tool
2. Position the clipping plane at the desired location
3. Enable Closed clip for a watertight result
4. Use Invert to toggle which half to keep
5. Click Apply

Splitting a Surface in Two

To divide a surface into two parts:

1. Position the clipping plane at the split location
2. Leave Closed clip off, so that Retain clipped region stays available
3. Enable Retain clipped region
4. Click Apply

Both halves are preserved as separate surface objects, each one open along the cut. To cap them, run the clip twice with Closed clip enabled instead, using Invert to keep the other half the second time.

Preparing for 3D Printing

To create a flat base for 3D printing:

1. Position the clipping plane parallel to the desired base
2. Enable Closed clip to create a solid, printable surface
3. Adjust Invert to keep the correct portion
4. Click Apply
5. Verify the result is manifold using Diagnostics and Fixes

Creating an Anatomical View

To expose internal anatomy:

1. Position the clipping plane at the desired viewing angle
2. Leave Closed clip disabled to see inside the structure
3. Click Apply

The open cut allows visualization of internal features.

Plane Positioning

Interactive Handles

The clipping plane widget provides interactive controls:

Handle	Action
Center sphere	Translate the plane in 3D space
Normal arrow	Translate along the plane normal
Rotation rings	Rotate the plane around its axes
Edge handles	Resize the plane visualization

Preset Orientations

Quick-set buttons (if available) align the plane to:

Orientation	Description
XY plane	Horizontal plane aligned with Plane 3 (XY)
YZ plane	Vertical plane orthogonal to X, aligned with Plane 1 (YZ)
XZ plane	Vertical plane orthogonal to Y, aligned with Plane 2 (XZ)

Best Practices

1. Use Closed clip for watertight results: If you need the clipped surface for 3D printing, simulation, or Boolean operations, always enable Closed clip.

2. Check manifoldness first: Closed clipping requires manifold input. Run diagnostics before clipping.

3. Preview before applying: The 3D view shows which portion will be retained. Verify this is correct before clicking Apply.

4. Use Retain for both halves: If you need both portions of the split surface, enable Retain clipped region.

5. Reset for alignment: Use Reset to center the clipping plane on your surface, then fine-tune from there.

6. Combine with other tools: After clipping, you may need to use Fill Holes or Smooth to refine the result.

See Also

• Cut - Trim using freehand and primitive ROI shapes
• Boolean - Compute Boolean operations between surfaces
• Fill Holes - Close open boundaries
• Diagnostics and Fixes - Verify and repair mesh quality