Selecting boundaries when machining solids with disk

I'm having an issue with my current project, I'm machining an stl onto granite and I need certain 2X4 sections to remain untouched while everything around gets machined. When I select both boundaries (2X4 and perimeter of stl boundary) while attempting 3D SOLID MACHINING it goes around the 2X4 section correctly and it works. Due to machining time its more efficient to do it with a disk, when I attempt selecting both perimeters for CUT SOLIDS WITH DISK I get an error message "BOUNDARIES MUST BE DISJOINT: THEY CANNOT INTERSECT/OVERLAPWITH EACH OTHER"

Is there a different way to do your boundaries when attempting solids with disk? Is there a way to do this?

I'm running alphacam stone

Thanks in advance!