The present invention provides 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. In one embodiment, the method includes etching a first substrate through a patterned mask layer in a plasma etch chamber, the first substrate having a backside disposed on a substrate support and a front side facing away from the substrate support, directing a first radiation source from the backside of the first substrate to a first area covered by the patterned mask layer, directing a second radiation source from the backside of the first substrate to a second area uncovered by the patterned mask layer, collecting a first signal reflected from the first area covered by the patterned mask layer, collecting a second signal reflected from the second area uncovered by the patterned mask layer, and analyzing the combined first and the second signal.