Thermal oxidation was used to remove the subsurface damage of silicon carbide (SiC) surfaces. The anisotropy of oxidation and the composition of oxide layers on Si and C faces were analyzed. Regular pits were observed on the surface after the removal of the oxide layers, which were detrimental to the growth of high quality epitaxial layers. The thickness and composition of the oxide layers were characterized by Rutherford backscattering spectrometry (RBS) and X-ray photoelectron spectroscopy (XPS), respectively. Epitaxial growth was performed in a metal organic chemical vapor deposition (MOCVD) system. The substrate surface morphology after removing the oxide layer and gallium nitride (GaN) epilayer surface were observed by atomic force microscopy (AFM). The results showed that the GaN epilayer grown on the oxidized substrates was superior to that on the unoxidized substrates.