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Molecular dynamics simulation combined with sophisticated visualization techniques may be one of the most powerful scientific tools for the study of atomic-level surface reactions during plasma-wall interactions. This paper shows visualization of an organic polymer model substrate before and during molecular beam injections. The classical interatomic potential model functions used in the present work are developed to describe chemical reactions, i.e., formation and breakup of chemical bonds under strongly nonthermal-equilibrium conditions. We have observed that, during beam injections, nonthermal-equilibrium chemical reactions take place in a nano-scale thin layer of the substrate top surface, which determines characteristics of the process, such as etching/deposition rates and selectivity.