A focused ion beam (FIB) system, fully computer controlled and containing a mounting stage with a laser interferometer, is used to investigate the accuracy of resist exposure fabrication and the mark detection. Fabricated patterns in poly(methylmethacrylate) (PMMA) and chloromethylated polystyrene (CMS) resists on both Si and SiO2substrates showed good pattern width accuracy. This appears to be because of the absence of the proximity effect in ion beam exposure and the stability of both the Au–Si–Be liquid metal ion source and the FIB system itself. The authors examine the use of Si, Be, and Au FIB’s for the detection of alignment marks covered with PMMA and CMS resists. Detection of marks covered with PMMA resist was possible because of the resist sputter etching produced by the FIB irradiation. For marks covered with CMS resist, the addition of a differential amplifier enabled successful detection here as well.