We have studied the influence of chemical sputtering effects on the morphology of carbon nitride films grown on silicon substrates by electron cyclotron resonance chemical vapour deposition. This study has been performed by comparing the evolution of their morphology with that of hydrogenated amorphous carbon films grown under similar conditions, where these effects are not present. When chemical sputtering effects operate we observe a film surface stabilization for length scales in the 60-750 nm range after a threshold roughness of about 3-4 nm has been developed. This stabilization is explained on the basis of the re-emission of nitrogen etching species, which is confirmed by growth experiments on microstructured substrates.