Abstract: The present invention provides a method for detecting Anomalous Substrates in Automated Material-Handling Systems comprising the following steps. A substrate cassette having at least one substrate is provided. The substrate cassette is positioned within the material handling system. Each substrate has a top surface and a bottom surface. A first beam is emitted from a first emitter wherein the first beam is in optical communication with the top surface of the substrate. A second beam is emitted from a second emitter wherein the second beam is in optical communication with the bottom surface of the substrate. The first beam and the second beam are detected using at least one detector.