For STLs there are a number of 3D CAM tools: MeshCAM, pyCAM, FreeMill, or importing the file into Autodesk Fusion 360 and using its CAM tools.
List of other options at: https://wiki.shapeoko.com/index.php/CAM#3D_2 and https://wiki.shapeoko.com/index.php/Commercial_Software#3D_C...