Remove Extra Faces on End Caps After Boolean in Blender

Delete the inner cylinder’s end caps, apply Scale/Rotation, and use the Boolean modifier’s Exact solver to avoid coplanar leftovers; if extra faces already exist, enter Edit Mode, select the tiny end‑cap faces (Select Similar by Area/Normal or Non‑Manifold), X > Only Faces, then Mesh > Clean Up > Merge by Distance and Limited Dissolve to rebuild a single clean cap. These blender boolean and boolean modifier blender steps (with face blender cleanup tools like Merge by Distance and Limited Dissolve) reliably remove stray end‑cap faces in Blender 5.0.1.

---

Contents

• Quick fix — blender boolean end-cap faces
• Step-by-step cleanup after applying Boolean (boolean modifier blender)
• Preventing extra end-cap faces (best practices)
• Advanced tips — selection, filling and thresholds
• Sources
• Conclusion

---

Quick fix — blender boolean end-cap faces

If you want the fastest route to a clean end cap:

• Before you Boolean: open the inner (subtractor) cylinder in Edit Mode and delete its top and bottom faces (Face select: 3 → select top/bottom faces → X → Faces). This prevents internal caps from being created.
• Apply transforms on both objects: Object → Apply → Scale & Rotation (Ctrl+A). Mismatched scale is a common cause of weird Boolean results.
• On the outer (thicker) cylinder add the Boolean modifier, set Operation = Difference, pick the inner cylinder, and set Solver = Exact (this handles coplanar faces better). See the official manual for the solver details: https://docs.blender.org/manual/en/latest/modeling/modifiers/generate/booleans.html.

If you’ve already applied the Boolean and you see extra faces on the end caps, do this right away:

1. Select the outer cylinder and go to Edit Mode (Tab). Switch to Face select (3).
2. Try Select > Select All by Trait > Non‑Manifold — that often picks internal stray faces. If that doesn’t catch them, click a tiny end‑cap face and do Select > Select Similar > Area (or Normal) to grab other small/coplanar faces.
3. Press X → Only Faces to delete just those internal cap faces without destroying surrounding topology. (This method is described in user fixes on Blender Stack Exchange: https://blender.stackexchange.com/questions/165043/boolean-operation-destroying-topology-deleting-faces.)
4. Clean up remaining geometry: Mesh → Clean Up → Merge by Distance (use a very small threshold like 0.0001) then Mesh → Clean Up → Limited Dissolve to collapse coplanar faces into a single cap.

---

Step-by-step cleanup after applying Boolean (boolean modifier blender)

Detailed sequence you can copy-paste into your workflow for the two-cylinder case you described:

1. Duplicate the outer cylinder first (Shift+D) so you have a backup.
2. Apply transforms on both objects: select each → Ctrl+A → Scale & Rotation. This avoids numerical precision errors during the Boolean.
3. With the inner cylinder selected, go to Edit Mode, enable Face select, select the top and bottom faces and press X → Faces to remove end caps. Leave the inner object as a hollow tube.
4. On the outer cylinder add Modifier → Boolean → Operation: Difference → Object: inner cylinder → Solver: Exact. If you already applied the modifier, skip to step 6. For live preview enable the modifier in Edit Mode to inspect before applying. Reference: https://docs.blender.org/manual/en/latest/modeling/modifiers/generate/booleans.html.
5. If the result looks good, Apply the Boolean modifier.
6. Enter Edit Mode on the result and run a cleanup chain:

• Mesh → Clean Up → Merge by Distance. Start with Distance = 0.0001 (for 1m scale) and raise it slowly if needed. This removes duplicate vertices created by the operation.
• Mesh → Clean Up → Delete Loose to clear isolated stray pieces.
• Select one of the tiny end faces and use Select → Select Similar → Area (or Normal) to capture all the small cap fragments, then X → Only Faces. (The “hide surrounding faces / delete only faces” trick is shown here: https://blender.stackexchange.com/questions/165043/boolean-operation-destroying-topology-deleting-faces.)
• With the hole now clean, select the rim edge loop (Alt+LeftClick on the rim) and either press F to fill with an ngon or use Face → Grid Fill for a quad grid. Adjust Grid Fill’s span to get nice topology.
• Finish with Mesh → Clean Up → Limited Dissolve to collapse coplanar faces and simplify the cap. You can control the Angle Limit if you want to keep sharper features.

Why these steps work: Booleans often create many small coplanar faces and duplicate vertices to guarantee manifold topology. Merge by Distance removes tiny duplicates; Limited Dissolve collapses coplanar faces to single larger faces; selective deletion of Only Faces lets you remove internal caps without taking away the rim or connecting edges. See community discussion and cleanup recipes here: https://blender.stackexchange.com/questions/75568/why-has-the-boolean-modifier-created-new-vertices and https://blender.stackexchange.com/questions/337011/mesh-clean-up-after-boolean-modifier.

---

Preventing extra end-cap faces (best practices)

A few habits will save you time:

• Delete end caps on the subtractor before Boolean. If the subtracting cylinder is an open tube the Boolean won’t generate those internal cap islands.
• Apply Scale & Rotation (Ctrl+A) to both meshes before the operation. Different object scales cause numerical edge cases.
• Use the Exact solver (Boolean modifier) for coplanar and precision cases — it’s slower but cleaner for end caps: https://docs.blender.org/manual/en/latest/modeling/modifiers/generate/booleans.html.
• Match topology density where possible. If the outer mesh is very dense and the inner one is low‑res, the Boolean can tessellate the cap in unexpected ways; try keeping subdivisions similar or do the Boolean on simpler geometry and retopologize. (Community advice: remove end caps or adjust subdivision before Boolean: https://blender.stackexchange.com/questions/22/how-do-i-do-a-clean-boolean).
• Slight offsets: if coplanar precision still gives trouble, nudge the subtractor by a tiny amount (scale by 0.999 or move 0.0001) to avoid exact coplanar overlap — but only as a last resort.

Do these before you apply the modifier and you’ll rarely need manual cleanup.

---

Advanced tips — selection, filling and thresholds

• Non-Manifold selection: Select > Select All by Trait > Non‑Manifold is a quick way to find internal faces, stray edges and open geometry left by a Boolean.
• Select Similar: clicking a small face then Select > Select Similar > Area is often faster than manual clicking when dozens of tiny cap fragments exist.
• Thresholds: Merge by Distance and Limited Dissolve both have sliders. Start very small (0.0001) and increase slowly — too large and you’ll collapse intended geometry.
• Rebuilding a cap: After deleting internal faces, select the rim edge loop (Alt+LeftClick) and use Face → Grid Fill for a structured cap; if you just want a simple flat cap, press F to make an ngon. Grid Fill is better if you want quads.
• If the Boolean produces a mess you can’t salvage, try doing the subtraction on a duplicate of the outer mesh with fewer subdivisions, then retopologize the result. The community has multiple practical workflows for this; see practical cleanup tips here: https://blenderartists.org/t/problem-of-boolean-modifier-and-way-to-clean-up-all-internal-geometry/1367310 and https://www.reddit.com/r/blenderhelp/comments/s97frx/how_to_properly_use_boolean_modifier/.

---

Sources

• Boolean Modifier - Blender 5.0 Manual
• Why has the boolean modifier created new vertices? - Blender Stack Exchange
• Boolean operation destroying topology — deleting faces - Blender Stack Exchange
• How to properly use boolean modifier? - r/blenderhelp (Reddit)
• Mesh clean up after Boolean modifier - Blender Stack Exchange
• How can I clean up Boolean operations? - Blender Stack Exchange
• How do I do a clean boolean? - Blender Stack Exchange
• Problem of boolean modifier and way to clean up all internal geometry - Blender Artists

---

Conclusion

For Blender 5.0.1 the quickest, most reliable fix for extra faces on end caps is prevention: delete the inner cylinder’s end caps, apply transforms, and use the Boolean modifier with the Exact solver. If artifacts already exist, remove them in Edit Mode with Select Similar or Non‑Manifold, X → Only Faces, then Mesh → Clean Up → Merge by Distance and Limited Dissolve, and refill the rim with F or Grid Fill. Do these steps and your blender boolean operations will produce clean end caps with minimal manual retopology.