A method and apparatus for inspecting specimens or patterned transmissive substrates, such as photomasks, for unwanted particles and features, particularly those associated with contacts, including irregularly shaped contacts. A specimen is illuminated by a laser through an optical system comprised of a laser scanning system, individual transmitted and/or reflected light collection optics and detectors collect and generate signals representative of the light transmitted by the substrate. The defect identification of the substrate is performed using those transmitted light signals. Defect identification is performed using an inspection algorithm by comparing image feature representations of a test specimen with a reference specimen, and using a boundary computer and flux comparison device to establish tight boundaries around contacts and compute flux differences between the test and reference specimen contacts. Defect sizes are reported as ratio of flux difference, and entire contacts are highlighted for review.