A charged particle beam system for processing substrates is disclosed, comprising a charged particle column, combination infrared radiation and visible light illumination and imaging subsystems, in-vacuum optics, and a precision stage for supporting and positioning the substrate alternately under the charged particle column and the imaging system. The axes of the charged particle column and imaging system are offset to enable much closer working distances for both imaging and beam processing than would be possible in a single integrated assembly. A method for extremely accurately calibrating the offset between the column and imaging system is disclosed, enabling beam processing at precisely-determined locations on the substrate. The imaging system is capable of locating sub-surface features on the substrate which cannot be seen using the charged particle beam. Two illumination modes are disclosed, enabling both bright-field and dark-field imaging in infrared radiation and visible light.
