Hi everyone. I redesigned my helmet base to use all quads and was working with a mirror modifier, then applied it. I then pulled up the 3d print tool box and found 66 non-manifold edges and then clicked “Make Manifold” and this was the result below. It created a couple of weird faces that greyed out the interior of the helmet that I can’t select inside of the helmet. Please advise.
It seems you original helmet has no thickness and so there were the non-manifold border found. This can not be printed (if it could then it also would be also only thin as paper 
… ). You should have used a solidify modifier and choose some thickness and apply it.
If this is meant for 3D-print then you might re-search some basics ? or: Why do you used the 3D-Print-Toolbox ??
Seems I’m putting one function before another lol, I just got ahead of myself. Thank you for the clarification. I stepped away from blender for a week and forgot some details. I just use the 3d print tool box mostly because I’m new to blender and it points out issues to me that my noob eyes can’t spot lol. I’m not always sure what issues will eventually arise in my slicer program when I get to that stage.
Should I apply my mirror modifier before creating a solidify modifier or does it really make any difference?
Not every “problem” is really a problem in some use cases 
…so if this is nt for 3D-print the non-manifold can be perfectly fine…
…according mirror-modifer: Try it. You can lean something… 
Usually one does mirror so any other modifier works one the resulting “complete” model.
It’s meant for 3d print. So I used a solidify modifier at 2mm thickness and then applied my mirror modifier and then pulled up 3d print tool box and it found 60 non-manifold edges. I clicked “Make Manifold” and this image was the result it gave me. Not sure what to do at this point as there is now thickness.
Okay, I see now. I just needed to apply the Solidify modifier. What suggestions could you give for fixing zero faces/edges?
Mesh → Merge → By Distance…
Okay, I merged up to 1 mm and checked Unselected and Sharp Edges, didn’t seem to do anything and zero faces are still there.
Hmm… that’s strange… zero faces are properly “narrower” than 1mm … ohh had you selected all vertices before merging ??
Yes, I typed A for select all and merged by distance and nothing changed. I even zoomed in, changed to wire frame mode to see if I could see extra vertices and even pulled the face outward and there was nothing there. I think there is something else going on that I’m not seeing here.
You might wanna upload the file ?? ( Only the helmet itself and using compress because of the 5MB limit here on BA…)
I can certainly try to, would copy and pasting the helmet base alone into a separate file be small enough? I’m not entirely sure how to compress files tbh
In the save dialog you can enable compress in the right panel
Overall I think your main problem is that you have nonmanifold coplanar overlapping faces on top of each other and the zero area faces are a subproblem of it. If its just for 3dprinting a voxel remeshing might be an easy solving option. But you’ll end up pretty hires that way.
How would I go about voxel remeshing? I’ve never heard of it.
Just go to sculpt mode. Its at the top of the viewport “Remesh”, choose a small voxel size. Save before you start.
infernohelmet2.blend (2.2 MB)
There’s the whole file if you want to take a look at it. I’m having a hard time finding remesh.
Had a quick look with another tool. Does seem to have no error. What tool did you use.
I know I’m probably trying to be a little too overzealous in zeroing out these checks but in all honesty/actuality, should I really worry too much about zero faces, thin faces, overhang, etc when it comes to pulling 3d models into a slicer program or for 3d print in general? Trying to discern how far to take my effort.
I am back in about half an hour. I can check it with print toolbox then aswell.