The modification of bundled single-walled and multiwalled carbon nanotubes is examined using a combination of computational and experimental methods. The computational approach is classical molecular dynamics simulations using the many-body reactive empirical bond-order potential parametrized by Brenner. The simulations consider the deposition of CH3+ at incident energies of 10, 45, and 80 eV. They predict the chemical functionalization of the nanotubes, the formation of defects on the nanotube walls, and the formation of cross-links between neighboring nanotubes or between the walls of a single nanotube. They also illustrate the manner in which the number of walls in the nanotube and incident energy affect the results. In the experiments, multiwalled nanotubes with about 40 shells (average diameter of 25 nm) are synthesized by chemical vapor deposition, CF3+ ions are deposited at incident energies of 10 and 45 eV, and then the nanotubes are examined with X-ray photoelectron spectroscopy and scanning electron microscopy. These experiments find strong evidence of chemical functionalization, in agreement with the simulation results.