The aluminum bedding block has to be milled down until it is the same thickness as the pillar height at the action screws, and so the bottom follows the contour of the top of the M-5 DBM. It's not easy. The best way, as previously mentioned, is to have it milled, gunsmith/machinist required. Preferably one who has done many before.
It can be done with a dremel tool but it's not as pretty. Usually you actually over cut with the dremel and then epoxy bed the DBM to the correct fit. Drill out the bedding block holes and epoxy in the pillars that come with the DBM.
If you love doing stuff yourself and don't mind it looking like that's just what you did, go for it.
If you care more about how your stuff looks and you'll go nuts worrying forever if it may not be right/looks weird just box the whole thing up and send it to GAP or someone else who has done hundreds. It will cost both money and time but will be rock solid.
