The chemical modification of polystyrene through the deposition of a beam of polyatomic fluorocarbon ions (C3F5+ and CF3+) at experimental fluences is studied using classical molecular dynamics simulations with many-body empirical potentials. To facilitate these simulations, a new C-H-F potential is developed on the basis of the second-generation reactive empirical bond-order potential for hydrocarbons developed by Brenner. Lennard-Jones potentials are used to model long-range van der Waals interactions. The incident energy of the ion beam is 50 eV/ion, and it is deposited normal to the surface. The simulations illustrate the important differences in the chemical interactions of these polyatomic ions with the polystyrene. The CF3+ ions are predicted to be more effective at fluorinating the polystyrene than C3F5+ ions, and the dissociation of the C3F5+ ions produce long-lived precursors to fluorocarbon thin film nucleation.