Embodiments of the invention include a method for forming alternating aperture phase-shift masks. An optically transparent substrate suitable for having a pattern of phase-shift regions formed thereon is provided. Alternatively, an opaque pattern is formed on the optically transparent substrate, the opaque pattern defining a pattern of phase-shift regions on the substrate. The phase shift regions are then ion implanted to damage the phase-shift regions. The damage penetrates to a predetermined depth and forms damaged regions that can be more easily etched than the adjacent undamaged portions of the substrate. The damaged portions define a final profile for phase shift recesses to be formed in the substrate. After implantation, substrate material is removed from the damaged phase-shift regions so that recesses are formed therein. The recesses are formed having a depth that corresponds to the depth of the damage caused in the phase-shift regions by the ion implantation.