The effect of high energy (85 MeV) nickel ions on diamond-like carbon thin films, deposited by microwave discharge of acetylene and methane gases mixed with hydrogen, has been investigated. IR, Raman and spectroscopic ellipsometry studies of irradiated and as-deposited films show large changes in their microstructural features. The effects of irradiation on films prepared from acetylene-hydrogen and methane-hydrogen gas mixtures are very different. Such a behaviour is proposed to be due to the microstructural variations in the as-deposited films.