We have measured at room temperature (RT) the Fourier-transform infra-red (FTIR) absorption spectra of ion-irradiated thin epitaxial films of cubic silicon carbide (3C–SiC) with 1.1 µm thickness on a 500 µm thick (1 0 0) silicon wafer substrate. Irradiations were carried out at RT with 2.3 MeV 28Si+ ions and 3.0 MeV 84Kr+ ions for various fluences in order to induce amorphization of the SiC film. Ion projected ranges were adjusted to be slightly larger than the film thickness so that the whole SiC layers were homogeneously damaged. FTIR spectra of virgin and irradiated samples were recorded for various incidence angles from normal incidence to Brewster's angle. We show that the amorphization process in ion-irradiated 3C–SiC films can be monitored non-destructively by FTIR absorption spectroscopy without any major interference of the substrate. The compared evolutions of TO and LO peaks upon ion irradiation yield valuable information on the damage process. Complementary test experiments were also performed on virgin silicon nitride (Si3N4) self-standing films for similar conditions. Asymmetrical shapes were found for TO peaks of SiC, whereas Gaussian profiles are found for LO peaks. Skewed Gaussian profiles, with a standard deviation depending on wave number, were used to fit asymmetrical peaks for both materials. A new methodology for following the amorphization process is proposed on the basis of the evolution of fitted IR absorption peak parameters with ion fluence. Results are discussed with respect to Rutherford backscattering spectrometry channeling and Raman spectroscopy analysis.