Molecular dynamics (MD) simulations are used for the study of non-thermal-equilibrium reactions that take place on the substrate surface during plasma etching processes. In MD simulations, the motion of each atom is solved numerically based upon pre-determined interatomic potential functions and data of interest (such as sputtering yields, deposition rates, etch products, etc.) are evaluated from statistical averaging of relevant instantaneous data obtained from the simulations. In the present work, MD simulations of organic polymer etching by hydrocarbon beams were performed and atomic-scale morphology of the substrate surface during the etching and its relation to sputtering yields were examined. Key words: molecular dynamics simulation; etching; deposition; plasma processing; organic polymer