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I've been able to track down add-ons for batch Obj import and batch STL export but I can't find one for batch STL import. Does anyone have a link to such an addon or have a python script?

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Start with importing obj file:bpy.ops.import_scene.obj

Then you export the scene with bpy.ops.export_mesh.stl : doc

After doing this, you need to delete all instance inside your scene and loop the process again. Should be a fairly easy add-on without tricky point.

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