Amorphous carbon films (a-C:H) and nitrogen incorporated carbon films [a-C:H(N)] deposited by a self-bias glow discharge have been implanted with 70 keV nitrogen ions at fluences of 0.6, 1 and 2×1017 N/cm2. The in-depth modifications caused by ion implantation were determined by means of nuclear techniques, such as Rutherford Backscattering Spectrometry (RBS), Nuclear Reaction Analysis (NRA) and Elastic Recoil Detection Analysis (ERDA), as well as by Auger Electron Spectroscopy (AES) and Raman scattering. ERDA profiles show that nitrogen implantation causes hydrogen depletion, the amount of which depends on the film composition and on the ion fluence. In a-C:H(N) films nitrogen loss was also measured. The induced structural modifications in both a-C:H and a-C:H(N) films were followed by both AES, using factor analysis, and microprobe Raman spectroscopy. They turn out to be related to the energy deposited by the incident ions. Our results indicate that the ion-beam bombardment causes in both a-C:H and a-C:H(N) films an increase of either the degree of disorder or the ratio between sp2/sp3 bonds across the hydrogen-depleted layer, which depends on the ion fluence.