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I know it is possible to select by trait interior faces and remove them, but when I am using modifiers, without applying I would not be able to do so, is there any way to clean the mess union modifier generate?

Sample: puzzle.blend

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there is new boolean algorithm in blender, so use the exact option in the boolean modifier if you are in b3d 2.91 to remove that overlapping geometry, but in 2.83-2.9 or older you have to remove those faces manually after applying the modifier...

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    $\begingroup$ I was using 2.83.5, I updated to 2.90.1 now but still there wasn't any fix, today 2.91 is beta, then I tried it and there was, fixed! $\endgroup$ Commented Oct 26, 2020 at 8:57

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