Very thin (<,100 nm) amorphous carbon films were grown on silicon substrates by unfiltered and filtered direct carbon ion beams. In situ surface modification was performed using C- energies in the range of 300–500 eV prior to the growth of the film. By lowering the energy of the C− beam to 150 eV, an amorphous carbon film was continuously grown after the surface modification. High-resolution electron microscopy showed that the film/substrate interface was damaged by 400 and 500 eV C− beams. The carbon composition profile at the interface investigated by electron energy-loss spectroscopy illustrated that the 500 eV C− beam generated a 30 nm thick carbon/silicon mixing layer at the interface. The damage and mixing layers were not observed at 300 eV modification. Wear testing found that strong adhesion occurred in samples modified at 400 and 500 eV. However, at 300 eV, modified samples exhibited delamination failure, which indicated inferior adhesion of the films. Surface roughness evolution of 30, 60, and 90 nm thick films was investigated by atomic force microscopy. The film surface roughness decrease as a function of film thickness was much faster when the films were grown by the filtered C− beam.