A system and method for inspecting a multi-layer sample, such as a silicon wafer, is disclosed. The design reduces variations in total reflected energy due to thin film interference. The design includes illuminating the sample at two incident angle ranges, where the two incident angle ranges are such that variation in total reflected energy at a first incident angle range may be employed to balance variation in total reflected energy at a second incident angle range. Defects are detected using die-to-die subtraction of the sample illuminated at the two incident angle ranges.