A hole of a hole size is cut in a composite material workpiece by selecting a milling cutter having an effective cutter size less than the hole size, mounting the composite material workpiece in operable relation to the milling cutter, rotating the milling cutter about an axis of rotation, and advancing the milling cutter longitudinally into the composite material workpiece parallel to the axis of rotation at a rate of longitudinal advance, while laterally moving the milling cutter perpendicular to the axis of rotation to interpolate the hole. The rate of longitudinal advance is controlled such that the hole remains substantially a flat-bottomed hole as it is cut. The composite material workpiece is desirably affixed to a backing fixture with an adhesive material during the cutting of the hole.