The underpinnings of two SIMS experimental findings are elucidated using the power of molecular dynamics to provide insight at the molecular level. First, the improvement of depth resolution for C60 bombardment of Irganox delta layers and polymer layers using sample rotation is explained by molecular dynamics simulations of the repetitive bombardment of Ag surfaces with 20 keV Au3, C60, and Ar872 at grazing angles of incidence with both single azimuthal angle and random azimuthal angles. Single azimuthal angle simulations at grazing angles show the formation of trenches and valleys parallel to the cluster beam form and are elongated with increasing incident angle. Cluster bombardment simulations with random azimuthal angles mimic sample rotation and show that under grazing angles of incidence, the surface is smoother because of the random impact angles preventing trench and valley formation. Second, depth profiles using C60 at a 70° angle of incidence have been improved by co-bombardment with low energy Ar ions emitted at 33° from the C60 beam and at a 45° incident angle from the surface. Molecular dynamics simulations of the bombardment of solid benzene with low energy Ar and 15 keV C60 were used to show the depth of damage created during bombardment. For low kinetic energy (<200 eV), the damage caused by the Ar atom is in the same region as for the C60 cluster. It is believed that for the experimental conditions used during co-bombardment, the Ar beam is breaking up the ridges created by the grazing C60 beam. Copyright © 2012 John Wiley & Sons, Ltd.