Classical molecular dynamics simulations are used to study the effects of continuous fluorocarbon ion beam deposition on a poly(vinylidene fluoride-trifluoroethylene) [P(VDF-trFE)] surface, a polymer with electromechanical properties. Fluorocarbon plasma processing is widely used to chemically modify surfaces and deposit thin films. It is well accepted that polyatomic ions and neutrals within low-energy plasmas have a significant effect on the surface chemistry induced by the plasma. The deposition of mass selected fluorocarbon ions is useful to isolate the effects specific to polyatomic ions. Here, the differences in the chemical interactions of C3F5+ and CF3+ ions with the P(VDF-trFE) surface are examined. The incident energy of the ions in both beams is 50 eV. The CF3+ ions are predicted to be more effective at fluorinating the P(VDF-trFE) surface than C3F5+ ions. At the same time, the C3F5+ ions are predicted to be more effective at growing fluorocarbon thin films. The simulations also reveal how the deposition process might ultimately modify the electromechanical properties of this polymer surface. (c) 2007 American Vacuum Society.