Molecular dynamics simulations are performed to model the nanomachining of materials via focused ion beams (FIBs). The goal of this research is to investigate the fundamental dynamics which govern the interaction of FIB with materials which are vital to the semiconductor industry, namely silicon. Specifically, we focus on the formation of trenches/holes within the sample and the dynamics responsible for their characteristic v-shape, as well as the extent of lateral damage due to a gallium beam. These phenomena have been successfully modelled, with evidence that the lateral and subsurface damage created is much larger than the beam itself. The results presented here begin to elucidate the dynamics governing the spatial resolution of these experiments, and provide an idea of some of the technical issues associated with these beams. (c) 2008 Elsevier B.V. All rights reserved.