The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms through integration of atomic equations of motion, using inter-atomic potentials that can account for bond breaking and formation that result when energetic species from the plasma impact surfaces. This article summarizes the current status of the technique for various applications of low temperature plasmas to material processing technologies. The method is reviewed, and commonly used inter-atomic potentials are described. Special attention is paid to the use of MD in understanding various representative applications, including tetrahedral amorphous carbon film deposition from energetic carbon ions; the interactions of radical species with amorphous hydrogenated silicon films; silicon nano-particles in plasmas; and plasma etching.