A focused ion beam (FIB) system has been used to implant and mill (100) Si with ion dosages ranging from 10 13 to 10 17 ions cm −2 , which are relatively low exposures compared to typical FIB applications. The topography of the resulting structures has been characterized using atomic force microscopy, including an analysis of edge effects. Conditions are presented for the controllable preparation of structures either protruding from, or recessed into, the surface by as little as 1 nm. Given the 10 nm lateral resolution of modern commercial FIB microscopes, direct nanofabrication for all three spatial orientations is therefore achievable.