A light beam collimated by illumination optics (4) from a radiation source (6) illuminates the surface of a wave front modulator (8) such as an Spatial Light Modulator (SLM) or Computer Generated Hologram photomask (CGH). The resulting wave travels via projection optics (10) to the substrate (12), passing through a projection lens assembly (14). The SLM (8) is programmed or CGH configured with a modulation pattern that is determined by the substrate (12) topography and desired pattern. The substrate topography is provided by Digital Holography (DH) surface profilometery performed by a DH microscope (18), which provides geometrical or topographical input to the CGH calculation routines (16). An arrangement for vertical or sloping surface patterning has a grating (22) superimposed onto the CGH pattern (24) to generate +1 and −1 orders. The SLM or CGH may be configured: using Fresnel patterns to provide an extended depth of field of the projected wave front; by encoding line segments of the desired pattern as cylindrical lines; by calculating inverse propagation between non-planar topography of the substrate and the SLM or CGH (using a Rayleigh-Sommerfield diffraction formula); and/or using iteration to determine a restricted encoding in the configuration of the SLM or CGH.