I have modified many dildos. Since I only buy silicone products, my comments are specific to that material - although I suppose they could work for others.

Cutting off a suction cup should be a simple task. The key is a very sharp knife - I prefer xActo knives. Be careful to always cut away from your body and fingers. Stretch the cup away from the base and make a firm slice with the sharp knife. Repeat the process until the suction cup has been completely severed.

I have also drilled a hole in the center of dildos to facilitate a 3/4" x 5" plastic vibe. It can be a little tricky, but nothing a reasonably accomplished handyman can't handle.