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I'm having an issue where a shape is non-manifold, but I don't know why, or how to fix it.

I've taken this below shape from inside another design by copying the vertices and making a new part (it's effectively a flush mount for a screw).

However, when I select the top circle of vertices and fill (and the same for the bottom), the shape becomes non-manifold. I noticed this when I tried to use this shape to cut out of a solid body and the faces didn't cut out like normal with a boolean difference operator.

Now, this shape is simple enough that I addressed it by recreating from scratch by extruding a cylinder and then scaling the top section. But I'd love to know what I could do it differently using the shape here.

From searching, common culprits look like normals pointing the wrong direction or double verts. I checked and normals are all pointing out. I checked and couldn't find any double verts (merged by distance just in case).

Suggestions? I'm new to blender, so appreciate the help!

Edit: Solved - the issue was that I ended up with double faces, so after capping it top and bottom I had internal faces. Deleting the internal faces solved the issue. I didn't fully understand manifold or normals - so when looking at normals (not shown in the below views for the non-capped version) - I should expect to ONLY see external normals. But I had internal normals as well, indicating internal faces as well!

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Edit: File link:

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  • $\begingroup$ Sorry, just by looking at it and since you seemingly have checked the usual suspects it is hard to tell what is wrong with it. You should probably upload the file so we can investigate it further - but I have an idea since I experienced it quite a few times: this terrible geometry looks like it was made with some kind of CAD software or whatever, at least I guess it was not made in Blender. Therefore you can have the following problem: it could be that three vertices not build one triangle, but two in the same place. This is usually not possible in Blender, but can be imported. $\endgroup$
    – Gordon Brinkmann
    Sep 12 at 9:57
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    $\begingroup$ "However, when I select the top circle of vertices and fill (and the same for the bottom), the shape becomes non-manifold." - either it doesn't become non-manifold as it already were (you can't add a face to a manifold mesh and keep it being manifold), or it indeed was manifold and so - as argued in my parentheses - it stopped to be. Here's an article about manifoldness: sculpteo.com/en/3d-learning-hub/create-3d-file/… $\endgroup$
    – Markus von Broady
    Sep 12 at 10:27
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    $\begingroup$ If it was manifold before you filled, and became non-manifold when you did, then it was probably double-skinned. After capping, you would have internal faces. $\endgroup$
    – Robin Betts ♦
    Sep 12 at 16:10
  • $\begingroup$ File added to the post. The way I made the geometry was taking it out of someone else's object, copying the vertices and making a new object from them. Almost certainly NOT made in Blender originally! $\endgroup$
    – Steve B
    Sep 13 at 11:02
  • $\begingroup$ "After capping, you would have internal faces" - this makes a lot of sense. Sorry, the manifold concept is relatively new to me, so I can see now that if I use the 3D print add-on to check for non-manifold and other issues and then to 'make manifold' without a top and bottom, then it creates internal faces as well - effectively double layering inside and outside. But then when I add a top and bottom, I've got internal faces, which create the issue. So going through and deleting the internal faces, should then result in a manifold shape. I'll test out that idea. Thanks! $\endgroup$
    – Steve B
    Sep 13 at 11:08

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You have overlapping faces, select all in Edit mode and press M > Merge by Distance (Merge Distance > 0.02), also recalculate the normals with ShiftN. Now you can fill the top and your object will be manifold.

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  • $\begingroup$ I though I'd tried that...though maybe only on vertices edit mode. I suppose in this case, I'd have to do edit faces mode and then try Merge by Distance? Does each edit mode (faces, edges, vertices) merge differently? Makes sense, just hadn't played with that! $\endgroup$
    – Steve B
    Sep 13 at 12:04

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