Masks can be repaired by creating a structure that is different from the original design, but that produces the same aerial image. For example, missing opaque material can be replaced by implanting gallium atoms to reduce transmission and quartz can be etched to an appropriate depth to produce the proper phase. In another aspect, a laser or other means can be used to remove an area of a mask around a defect, and then mask structures, either the intended design structures or alternate structures that produce the same aerial image, can be constructed using charged particle beam deposition and etching. For example, an electron beam can be used to deposit quartz to alter the phase of transmitted light. An electron beam can also be used with a gas to etch quartz to remove a layer including implanted gallium atoms. Gallium staining can also be reduced or eliminated by providing a sacrificial layer that can be removed, along with the implanted gallium atoms, using, for example, a broad ion beam. In another aspect, a charged particle beam can be programmed to etch a defect using three-dimensional information derived from two charged particle beams images of the defect from different angle.