I have created a Solid Cylinder in Rhino that shows there as a Solid Polysurface and saved it as a file.
I created an extrusion in Grasshopper, then using the File Path/Import 3dm tools, I perform a Solid Difference between the GH extrusion and the file-referenced, solid cylinder.
The result appears to cut a surface through the extrusion not taking out the inside of the hole that the solid cylinder should cut.