I just started 3d modeling with Blender about 3 weeks ago. Steep learning curve but I was able to muddle along (thanks to this site). Now I am stuck. I am volunteering at a non-profit and I have to modify an existing container that has some openings in the bottom to allow wires to pass through. I received this as an STL file (I think from AutoCad). I need to fill in a portion of some of these openings. The openings and my patch are non-uniform in shape but should be the same depth (along z axis). I tried making a face in the opening and solidifying it down until it was the same depth as the existing opening. I guess I thought this would magically become part of the existing mesh and I would have the new smaller opening. Well, I had a lot of non-manifold edges.

I finally backed down to a simple test case to try to understand what was going wrong. I made a simple frame 50mm x 50mm and a depth of 5mm. This was made by applying a difference boolean to two Blender cubes. I then tried to make a "beam" go from one side of the frame to another on the y-axis. First I tried subdividing the two edges on the top and using those 4 vertices to make a face which I solidified downward to the same 5mm depth. This gave me non-manifold edges with the "multiple faces" selected. I figured this was because of the hidden faces at each end of the beam. So, I was able to delete the faces on each end of the beam but the original frame face was still inside.

I then tried again from scratch. This time I put two edge loops on the inside of the frame across from each other along the y-axis. I selected those two faces and deleted them. This was going to be where the face of the solidify object would wind up so I thought it had to go. I then did the same face solidify and then deleted the face on each end of the new beam. Now I get non-manifold edges with the "boundaries" check box.

Here is what Blender looks like now.

enter image description here I am at a loss. I must be missing something pretty fundamental. I thought filling in a hole like this would be easy but I can't find any examples of someone modifying an existing object like this.

Here is my blend file.

Any help would be much appreciated.



Update: I was still messing around and found that the "Make Manifold" option in 3d print fixes it. So, I must be close. Really want to understand what is going on here.

Follow up image enter image description here

Final Update: lemon was able to solve my issue and in doing so he shared a very great diagnostic/debugging technique which I hadn't seen in all my previous searches. I wanted to make sure to point it out for any beginners following me up the Mt. Everest of learning curves. ;-)

If you are having problems with an area of your mesh the 3d print tools or select non-manifold geometry will indicate the basic area but it can be hard to see what is going on. From lemon's answer and his image I learned the following..don't be afraid to grab a vertex or edge or scale a face. Move it around and it will be obvious what it is and isn't connected to. You can always do a RMB or ctrl-z to put it back when you are finished looking. I have been working on a more difficult variation this afternoon and using this technique I have gotten to 0 non-manifold geometries every time (eventually).

Thanks for the tip, lemon!

  • $\begingroup$ Hello :). Please add a sketch of your desired outcome. "I need to fill in a portion of some of these openings." is rather vague :). $\endgroup$ Nov 1, 2020 at 6:58
  • $\begingroup$ @Jachym Michal, my posted image was my desired outcome. The mesh looked ok but had non-manifold geometry so it wouldn't print. $\endgroup$
    – DonC
    Nov 1, 2020 at 22:50

1 Answer 1


The reason.

The non manifold part comes from the bottom face of the "bridge".

You can see that if you select the face and scale it down:

enter image description here

Its sides are not linked to the main part of the mesh.

Few modifications in the file above, so that all faces are quads.

  • $\begingroup$ I downloaded my original blender file and scaled the top face and it looked like it was attached to the frame (see new image). I thought it would be since there are two vertices at the corners on the face and frame. Anyway, your blender file is correct but I can't go from mine to yours. Would you please give me a list of steps to performed? $\endgroup$
    – DonC
    Nov 1, 2020 at 17:10
  • $\begingroup$ @DonC, I was talking about the bottom face. For the other aspects simply made quad joining vertices. $\endgroup$
    – lemon
    Nov 1, 2020 at 17:12
  • $\begingroup$ ok now I see...the bottom face is indeed disconnected. Sorry for being a blender nooby but I tried to wire in the bottom two vetices on each base face and was not able to connect them to the bottom frame edge. I thought if I placed the vertices on the edge (with snap enabled) that they would connect to the edge. How do I connect them to that edge? $\endgroup$
    – DonC
    Nov 1, 2020 at 18:33
  • $\begingroup$ in all my messing around my auto merge had gotten turned off. When I re-enabled it I was able to snap the bottom vertices on the beam face to the frame vertices. Still have a lot of things to work out in my mind...my version doesn't look as clean as yours but three weeks ago I thought Blender was something to mix margaritas in. :-) I will take 0 non-manifold errors at this stage. Thanks again. $\endgroup$
    – DonC
    Nov 1, 2020 at 18:44
  • $\begingroup$ @DonC, great. It is good to see you've found several things by yourself. Also, cannot explain all myself for every case here, but it seems you are doing well. Feel free to ask for a specific problem (here in comments or by another question). $\endgroup$
    – lemon
    Nov 1, 2020 at 18:51

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