Simulations and experiments have found that at incident energies of 10-80 eV/ion, ion deposition on carbon nanotube bundles leads to covalent bond formation between nanotubes or adjacent tube walls. In this study, classical molecular dynamics simulations are used to study the polyatomic-ion beam deposition on C60-filled carbon nanotubes (nanopeapods). The ion beam consists of 10 CF3+ ions and the incident energy considered is 80 eV/ion. The system consists of a bundle of (10,10) single-walled carbon nanotubes filled with C60 molecules. The forces in the simulation are calculated with the short-ranged many-body, reactive empirical bond-order potential for hydrocarbons and fluorocarbons and long-range Lennard-Jones potentials. The simulations confirm the effectiveness of ion beam deposition in producing covalent cross-links between the carbon nanotubes and the C60 molecules. They also predict the dependence of such modifications on the location of the nanotube within the bundle relative to the ion beam from an atomic-scale point of view. The findings could have important implications for the production of carbon nanotube-based nanocomposites materials and electronic devices.