In this report we investigate the effects of focused ion beam (FIB) machining at low doses in the range of 10 15 ions/cm 2 to 10 16 ions/cm 2 for currents below 300 pA on Si(100) substrates. The effects of similar doses with currents in the range 10pA to 300 pA were compared. The topography of resulting structures has been characterized using atomic force microscope, while crystallinity of the Si was assessed by means of Raman spectroscopy. These machining parameters allow a controllable preparation of structures either protruding from, or recessed into, the surface with nanometre precision.2