Rapid thermal annealing (RTA) has been performed on the carbon films prepared by radio frequency plasma-enhanced chemical vapor deposition on Si substrate. The RTA at 800 °C for 60 s leads to the formation of many diamond nanocrystallites agglomerating on the film surface. Higher temperature RTA at 1100 °C for 60 s induces the high-density amorphous SiOx (x = 1.2) nanowires on the film surface without diamond nanocrystallites. At both the RTA temperatures, a well-oriented SiC interlayer is also formed simultaneously. The sp3 sites in the carbon film and the oxygen during the RTA treatment as well as the RTA temperature are considered to play important roles in determining the final reaction products.