Molecular dynamics methods are used to model the impingement of low energy ions onto crystalline targets, and the effects of these beams on thin film deposition. Simulations of the deposition of silicon films show that the structure of deposits can often be improved by the use of low energy ion beams instead of the conventional thermal beam. We examine the influence of beam energy on the formation of amorphous or crystalline deposits. The influence of ion beams on surface diffusion rates and the interdiffusion between atomic layers near the surface are also considered. Cluster deposition is treated, and the results suggest that cluster beams would be effective for depositing smooth films of materials that do not wet the substrate. We discuss the use of special purpose computers and signal processing boards to extend the time scales of molecular dynamics simulations. Rapid advances in computer hardware, algorithms, and the development of accurate interatomic potentials are dramatically increasing the power of these simulations.