The machining response of amorphous and crystalline Ni78B14Si8 was investigated when structuring substrates using focused-ion-beam (FIB) milling. In particular, the sputtering yield as a function of the scan speed, and the effects of ion fluence and scan speed on the milled depth were studied. The ion fluence dependent evolution of the cross-sectional profiles of trenches was examined by atomic force microscopy (AFM). When milling amorphous Ni78B14Si8 it was found that the sputtering yield first decreased with increasing the beam scan speed, then kept constant within the scan speed range, up to 710 nm/s, investigated in this work; it was also found that the milled depth was almost proportional to the ion beam fluence. The patterning of polycrystalline Ni78B14Si8 resulted in anisotropic milling-rates due to the varying orientation of the grains in the material. The analysis of the profile evolution in both materials indicated that the surface finish of trenches was scan speed, ion beam fluence and scan strategy dependent. The study demonstrated that direct patterning by FIB could be used for producing masters in amorphous Ni-based alloys for injection moulding and hot embossing. (C) 2006 Elsevier B.V. All rights reserved.