The repair of opaque defects in photomasks and reticles using focused ion beams (FIBs) can give rise to staining of the quartz substrate. A purpose built system is used to measure the transmission properties of stained regions and reveals relative fractional transmission of 60% at i line, falling to 25% in the deep ultraviolet (DUV). A series of printability trials using commercial steppers and processes at i line and DUV wavelengths shows the effects in resist images due to these stains in comparison with the original defects. The negative resist process used at DUV affords some protection against the printability of stained areas. However, the results confirm that antistain processes must be used with FIB repair which can be counter productive without them.