Abstract: Protecting the transparent substrate of a photomask when repairing opaque defects of the mask is disclosed. The photomask includes an opaque defect on a transparent substrate. The photomask is coated with photoresist. The mask is backside-exposed to a light source, to expose the photoresist where it is unblocked by the mask's opaque defect and other opaque regions. The photoresist is removed where it was unexposed to the light source. The opaque defect and the other opaque regions of the mask are exposed through the photoresist, but the transparent regions of the mask—where the transparent substrate does not have the opaque defect or the other opaque regions thereon—remain protected by the photoresist. The opaque defect is then removed, such as by using a focused ion beam (FIB). The photoresist over the exposed transparent substrate protects the substrate from riverbed effects and gallium staining.