Hi Author,
In OpenCASCADE, boolean operations (section, cut, common, fuse) are performed over TopoDS_Shapes with classes available from the BRepAlgoAPI package. You can use the StlAPI package to open/parse/convert the STL file to a TopoDS_Shape, and then perform any available boolean operation. I don't see any problem a priori (I never tested boolean ops with STL files), but you might face topological issues (due to the poor topological quality coming from the triangle based description of STL).
Regards,
Commenter-1