Fixing Invisible Holes: How to Find and Merge Duplicate Vertices

Your model looks solid, but it’s behaving strangely. The Subdivision Surface modifier creates weird tears and pinching, smooth shading has unexpected creases, and you might even have faces that you can’t seem to select properly. You’ve checked for flipped normals, but that’s not the problem.

The likely culprit is one of Blender’s most common hidden issues: duplicate vertices. These are multiple vertices stacked in the exact same location, creating invisible breaks in your mesh that cause all sorts of problems.

What’s the Cause?

Duplicate vertices are easy to create by accident, especially when you’re new to Blender. The most common cause is an accidental extrusion. If you press E to extrude and then right-click or press Esc to cancel the movement, the new geometry is still created, just left in the exact same position as the original. Importing models from other software can also sometimes result in duplicated geometry.

The Diagnosis: You Can’t Fix What You Can’t See

Unlike flipped normals, there isn’t a colorful overlay to spot duplicate vertices. The best way to know you have them is by their symptoms—bad shading and modifier glitches. The definitive way to confirm the issue is to perform the cleanup operation itself and see if it finds anything to fix.

The Cure: Merge by Distance

Blender has a powerful and simple tool designed specifically for this problem. It finds any vertices that are on top of each other (or very close) and merges them into a single vertex, welding the “invisible holes” in your mesh shut.¹

1. Select your object and press Tab to enter Edit Mode.
2. Press A to select all the vertices in your model.
3. Press the M key to bring up the Merge menu.
4. Select By Distance.

Look at the bottom status bar of the Blender window. You will see a small message that says, “Removed X vertices.” If that number is greater than zero, you’ve successfully cleaned your mesh. Your shading and modifier issues should now be resolved. This simple cleanup is a vital step for maintaining a healthy, problem-free model.