[Gmsh] Modification of .stl file

[Dimitrios Eftaxiopoulos]

Hello,
I have an .stl (or .vtk or .vtp) closed surface file and I have successfully 
meshed the volume of it, in a variety of ways, using gmsh. Now I want to 
create circular cylindrical holes on it. To the best of my knowledge, this is 
not possible in a straightforward manner, due to the limitations of 
information included in the .stl file (just surface triangles). I tried to 
drill a simple cube.stl surface using gmsh, at no success.

Most probably I have to convert the .stl file to another cad file format, like 
the open formats .iges, .step or .brep and open the holes on this file, using a 
cad package. I have tried FreeCAD, but the conversion to .brep results in an 
empty file.

Can anyone suggest a way and a tool for modifying an .stl file?

Regards
Dimitris