Rick, I had the same problem when I first started making sheaths. I solved it (for me) by resting the side of the sheath being drilled on a 1/4" thick piece of wood or micarta. This seemed to square things up considerably, although I still have to keep my eye on the edge of the sheath to make sure it is staying perpendicular to the drill bit. I also place a piece of paper towel over the board and the drill press table to keep the sheath clean, and drill through both the towel and the board.