Molecular dynamics (MD) simulations are used to study non-thermal-equilibrium reaction dynamics taking place on the surface during dry 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 this paper, we review our recent MD simulations results on organic polymer etching. Similar simulations were also performed for selective etching processes of silicon and silicon dioxide substrates.