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I'm looking for a piece of software for Windows or Linux that can compare how two 3D models differ.

It should preferebly be lightweight piece of free software, but I'm in hearing other options.

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CloudCompare seems to be a good choice to do the compare.

(ScreenShot) With Nice Color range indicate areas been changed and how much are changed

I manage to use Autohotkey to automate the process and post the detailed setup in CloudCompare official forum:

Use CloudCompare as Git diff tool to check model difference - CloudCompare forum http://www.cloudcompare.org/forum/viewtopic.php?f=9&t=4969

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