In this paper, we provide an overview of the use of molecular dynamics for simulations involving energetic particles (Ar, F, and CFx) interacting with silicon surfaces. The groups (including our own) that have performed this work are seeking to advance the fundamental understanding of plasma interactions at surfaces. Although this paper restricts itself largely to the systems bracketed above, the approach and general mechanisms involved are applicable to a much wider range of systems. Proper description of plasma-related systems generally requires a large number of atoms in order to correctly characterize the interactions. Consequently, the bulk of the present work, and the main focus of the text, is based on classical molecular dynamics. In MD simulations, one of the most critical considerations is the selection of the interatomic potential. For simulations involving silicon etching, the choice is typically made between the Stillinger-Weber and the Tersoff-Brenner potentials. An outline of the two potentials is given, including efforts that have been made to improve and optimize the potentials and their parameters. Subsequently, we focus on some of the practical details involved in establishing the simulation process and outline how various parameters (e.g. heat bath, relaxation time and cell size) influence the simulation results. These sections deal with the influences of the heat bath (application time, rising time), the time-step and total integration time of molecular trajectories, the relaxation of the sample (during and post-etching) and the sample size. The approach is essentially pedagogical in nature, and may be of interest to those less familiar with the techniques. To illustrate the type of results that can be produced we present a case study for 100 eV CF3+ interacting with a Si(100)-2x1 surface at different sample temperatures (100-800 K). The simulations reveal details of the change in etch rate, the F-turnover and the standing coverage of functional groups as a function of the temperature. Our primary interest is in studies with relevance for plasma-surface interactions. We discuss the general mechanisms that are most important in plasma-surface interactions and give an overview of some of the wide range of results that have been produced for various systems. The results presented illustrate that careful consideration must be given to the precise configuration of the plasma system. Numerous factors, including the chemical species, the energy and chemical mix of the incident particles and the surface composition and structure can play a crucial role in determining the net outcome of the interaction.