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I've tried to select all, remove faces, invert from another post etc... however my faces still overlap. It's one mesh, here's a photo. The overlapping is very apparent where the objects intersect.

enter image description here

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    $\begingroup$ if you've removed doubles and it begins to destroy your mesh, I'm afraid you need to correct your mesh manually $\endgroup$ – moonboots Jul 3 at 14:59
  • $\begingroup$ It doesn't destroy the mesh, it just doesn't do anything at all. $\endgroup$ – Centaurus Jul 3 at 15:05
  • $\begingroup$ so I guess you need to work manually, maybe share your file $\endgroup$ – moonboots Jul 3 at 15:08
  • $\begingroup$ Okay, I'll add it to the main post. Do I just upload it to Mediafire? $\endgroup$ – Centaurus Jul 3 at 15:11
  • $\begingroup$ blend-exchange.giantcowfilms.com and put the URL of this page before uploading $\endgroup$ – moonboots Jul 3 at 15:35
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Your topology is not good, for example when you cross two parallelepipeds you don't just duplicate one and rotate it 90°, you need to create edge loops, extrude or bridge, etc... so that faces don't overlap. Also try to work with quads.

Note that in some cases it's ok to just intersect meshes (for example if the pieces don't need to appear welded).

enter image description here

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