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I need to compare two STL (Dental model Scanned) files and find the deviation between their points, SO this two STL files have different boundary, so i already used the GEOMAGIC Control software for comparing STL files, one sample output file would be like this: enter image description here

I found these two like:

Are there any open source alternatives for geomagic?

How to compare/quantify (populate) two .stl models having shape difference to see result as color stl file and bar telling plus and minus changes?

useful for finding free alternative software for Geomagic, So i installed the Cloudcompare in my Linux OS, and aligned two stl file and used the compute cloud/mesh distance icon and get this output picture of stl which shown geomagic output above:

enter image description here

So in the CloudCompare output i have 1 aria which i don't want to be. How could i solve this problem?

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I found the reason, i must use other stl as references and the out put have this kind: enter image description here

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