Abstract: A method and apparatus for a charged particle scanning system and an automatic inspection system, including wafers and masks used in microcircuit fabrication. A charged particle beam is directed at the surface of a substrate for scanning that substrate and a selection of detectors are included to detect at least one of the secondary charged particles, back-scattered charged particles and transmitted charged particles from the substrate. The substrate is mounted on an x-y stage to provide at least one degree of freedom while the substrate is being scanned by the charged particle beam. The substrate is also subjected to an electric field on it's surface to accelerate the secondary charged particles. The system facilitates inspection at low beam energies on charge sensitive insulating substrates and has the capability to accurately measure the position of the substrate with respect to the charged particle beam.