This is a trivial problem for the drill tool. Simply drill a hole through and then drill a bigger hole down to the depth you want. I think your bigger problem is to get a nice smooth surface on your pattern. I think scanning is just too crude. You will be left with too much hand finishing to do. I would either create the grip from scratch in Designer or create a STL in other software and import it into Designer. You can get much help here from the forum, but you have to post stuff for us to play with!
Do search 1911 grips if you have not.