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I have little experience with CAD software, only use Thinkercad and only recently started using the Revoscan app. I know how to rotate files when slicing (in Cura) but that only has an effect on the generated gcode file, not the STL/OBJ file. But as I'm trying to publish a few things I scanned using Kiri Engine (photogrammetry app) where the original rotation is wrong.

I want to know if I have an object in OBJ/STL format how do I rotate the position in those files so I can publish my OBJ/STL files in the proper rotation. I'm fine to use another app or tool, I just don't know how to do it yet.

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Many 3D editing programs exist that will accomplish your objective. Tinkercad will do this as well, using the rotate feature, followed by moving it to the build plane and exporting it as an STL as desired.

Fusion 360 is available for free personal use, but has a bit of a learning curve.

Meshmixer from Autodesk will also rotate in the x/y/z axes and also place the model on the build plane.

You've presented your objective well enough. I suggest to pick a single program and ask specifically how to accomplish that which you are unable to achieve.

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