Multicharged ions (MCIs) produced in a new, electron beam ion trap (EBIT) based ion source, were investigated as a means of inducing athermal surface reactions for thin film processing. The specific surface systems investigated were highly oriented pyrolytic graphite (HOPG), nanodiamond (ND) and polycarbonate (PC). Beams of oxygen (Q=3+ and 5+) and argon (Q=1+, 4+, and 8+) ions were focused at normal incidence onto these target surfaces with fluences in the range of 1012 1013 particles per square centimeter. In-situ measurements of desorption and ex-situ measurements of surface modifications using mass spectrometry, Raman spectroscopy and XPS were made to determine ion-induced effects. The primary ion-induced results were in the HOPG and PC systems, where the ion impacts led to structural changes that could be attributed to bond breaking (both HOPG and PC) and the formation of new solid phases (HOPG to diamond-like conversion). The structural changes observed in PC indicate a charge-dependent enhancement, and, consequently, dose-dependent effects with an onset at fluences three orders of magnitude below those required for singly charged ions surface processing of the same substrate.