Ion beam simulation techniques are used to study fluorocarbon residue formation and substrate composition and structure modifications of silicon by CHF3 plasma environment. Fluorocarbon residues are shown to grow by direct ion incorporation or ion activated growth processes in ion beams over the energy range 50–1000 eV. At ion energy >150 eV concurrent sputtering of the overlayer film results in a steady state film thickness of ∼30 Å, relatively independent of ion energy. Films are fluorine deficient, with C/F ratio of 1–3 depending on ion energy, dose, and film thickness. Energetic ion (300 eV) penetration of the film results in continuous Si etching and substantial substrate modification. For 560 eV ion energy an ion-mixed interfacial layer of approximately 25 Å thickness is produced which contains substantial O, C, and F. A deeper (>150 Å) damaged layer is observed due to H+ implantation. Removal of overlayer films and interfacial layers by standard cleaning procedures is addressed.