Molecular dynamics simulations are performed to model milling via a focused ion beam (FIB). The goal of this investigation is to examine the fundamental dynamics associated with the use of FIBs, as well as the phenomena that govern the early stages of trench formation during the milling process. Using a gallium beam to bombard a silicon surface, the extent of lateral damage (atomic displacement) caused by the beam at incident energies of both 2 and 30 keV is examined. These simulations indicate that the lateral damage is several times larger than the beam itself and that the mechanism responsible for the formation of a V-shaped trench is due to both the removal of surface material, and the lateral and horizontal migration of subsurface silicon atoms toward the vacuum/crater interface. The results presented here provide complementary information to experimental images of trenches created during milling with FIBs.