A scanning electron-beam lithograph machine (CUMMS 11) is described, which utilizes a novel back wafer registration technique (BWR). The registration method uses two axially coincident electron beams—one of which addresses the back of the wafer and is used for registration, the other addresses the top chip surface and is used for pattern writing. By reading a matrix array of BWR marks the system recognizes wafer distortions and provides compensation in subsequent pattern writing. An extension of this process allows stitching of subfields for writing large area chips. Since the system is symmetrical with the writing and registration occurrring on the same axis, temperature drifts are insignificant. Also several electronic drifts are self-compensating. Also several electronic drifts are self-compensating. The BWR method is ideally suited to use with shaped electron beam writing optics and may also be used for registration in ion-beam writing or selected area electron-beam annealing systems.