Trying to fill an opening in an object and match depth 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 &quot;beam&quot; 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 &quot;multiple faces&quot; 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 &quot;boundaries&quot; check box.
Here is what Blender looks like now.

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.
Thanks,
Don
Update: I was still messing around and found that the &quot;Make Manifold&quot; option in 3d print fixes it. So, I must be close. Really want to understand what is going on here.
Follow up image

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!
The reason.
The non manifold part comes from the bottom face of the &quot;bridge&quot;.
You can see that if you select the face and scale it down:

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

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