In the FSDS3 help, click on the "Search" tab and type in "Boolean".

The first item that comes up "Boolean OPerations" is a good tutorial by Graham Oxtoby on cutting out a wheel well from a wing.

The basics are:

Create a die part tagged "tool"

move it into position to intersect the part you want to cut into....

select both the part and "tool"  ONLY.

execute the boolean operation  (CTRL-B)

Clean up - discard unneeded parts created, etc.