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Say I joined multiple objects together (instead of boolean), the meshes are now overlaping each other. Instead of selecting the faces/verticies one by one, split them into objects and combine them back into one mesh with boolean modifier, is there a smarter way of achieving the same thing(delete concave/intersecring/overlaping faces inside)?

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Go to Edit Mode, then press P (mnemonic: seParate) and choose "Loose parts". That'll undo the join, and produce an object for each part of your mesh.

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