A method and apparatus for inspecting patterned transmissive substrates, such as photomasks, for unwanted particles and features occurring on the transmissive as well as pattern defects. A transmissive substrate is illuminated by a laser through an optical system comprised of a laser scanning system, individual transmitted and reflected light collection optics and detectors collect and generate signals representative of the light transmitted and reflected by the substrate. The defect identification of the substrate is performed using only those transmitted and reflected light signals, and other signals derived from them, such as greyscale representations and image features. Defect identification is performed using a pattern inspection algorithm by comparing image feature representations of the present substrate with an idealized representation thereof, and using an advanced phase shift algorithm that accounts for particular types of expected anomalies.