A method and apparatus for etching a photomask substrate with enhanced process monitoring, for example, by providing for optical monitoring at different regions of the photomask to obtain desired etch rate or thickness loss is provided. In one embodiment, the method includes performing an etching process on a reflective multi-material layer that includes at least one molybdenum layer and one silicon layer through a patterned mask, directing radiation having a wavelength from about 170 nm and about 800 nm to an area of the multi-material layer uncovered by the patterned mask, collecting an optical signal reflected from the area uncovered by the patterned mask, analyzing a waveform obtained from the reflected optical signal, and determining a first endpoint of the etching process when an intensity of the reflected optical signal is between about 60 percent and about 90 percent less than an initial reflected optical signal.