Hard amorphous fluorinated carbon films (a-C:F) deposited by plasma enhanced chemical vapor deposition were annealed in vacuum for 30 min in the temperature range of 200–600 °C. The structural and compositional modifications were followed by several analytical techniques: Rutherford backscattering spectrometry (RBS), elastic recoil detection analysis (ERDA), x-ray photoelectron spectroscopy (XPS) and Raman spectroscopy. Nanoidentation measurements and lateral force microscopy experiments were carried out in order to provide the film hardness and the friction coefficient, respectively. The internal stress and contact angle were also measured. RBS, ERDA, and XPS results indicate that both fluorine and hydrogen losses occur for annealing temperatures higher than 300 °C. Raman spectroscopy shows a progressive graphitization upon annealing, while the surface became slightly more hydrophobic as revealed by the increase of the contact angle. Following the surface wettability reduction, a decrease of the friction coefficient was observed. These results highlight the influence of the capillary condensation on the nanoscale friction. The film hardness and the internal stress are constant up to 300 °C and decrease for higher annealing temperatures, showing a direct correlation with the atomic density of the films. Since the thickness variation is negligible, the mass loss upon thermal treatment results in amorphous structures with a lower degree of cross-linking, explaining the deterioration of the mechanical properties of the a-C:F films.