There is disclosed numerous embodiments of a method and apparatus for a particle scanning system and an automatic inspection system. In each of these a particle beam is directed at the surface of a substrate for scanning that substrate. Also included are a selection of detectors to detect at least one of the secondary particles, back-scattered particles and transmitted particles from the substrate. The substrate is mounted on an x-y stage to provide it with at least one degree of freedom while the substrate is being scanned by the/particle beam. The substrate is also subjected to an electric field on it's surface to accelerate the secondary particles. The system also has the capability to accurately measure the position of the substrate with respect to the charged particle beam. Additionally, there is an optical alignment means for initially aligning the substrate beneath the,particle beam means. To function most efficiently there is also a vacuum means for evacuating and repressurizing a chamber containing the substrate. The vacuum means can be used to hold one substrate at vacuum while a second one is being loaded/unloaded, evacuated or repressurized. Alternately, the vacuum means can simultaneously evacuate a plurality of substrates prior to inspection and repressurize of the same plurality of substrates following inspection. In the inspection configuration, there is also a comparison means for comparing the pattern on the substrate with a second pattern.