I think it was Justin Presson or Anthony Self who made a drilling jig for just this problem. If you search the archives under "drilling jig" I think you'll find it. I can't remember off the top of my head what the thread was titled.
In a nutshell, they took a piece of square tubing or c-channel with a clearance hole in the top and clamped the scale inside with the flat side up against the tubing. Your drill mark will show through the clearance hole in the tubing. This way you're drilling down into the bottom side of the scale, which is pointing upward and held flat. The odd shaped bumpy surface of the scale is taken out of the equation.