A semiconductor substrate inspection system includes an e-beam inspection system configured to deliver electrons to a specimen semiconductor substrate. A sensor is configured to detect reflected electrons that reflect off the surface of the specimen semiconductor substrate. An analysis unit is configured to determine a number of electrons received by the semiconductor substrate, and to determine at least one target region including at least one defect of the semiconductor substrate. A reference image module is in electrical communication with the analysis unit. The reference image module is configured to generate a first digital image having a plurality of pixels, and to adjust a gray-scale level of the pixels included in the target region based on the number electrons included in each pixel to generate a second digital image that excludes the at least one defect.