We investigate by means of Atomic Force Microscopy and Scanning Electron Microscopy the surface modifications of 3C-SiC(111)/Si epilayers induced by thermal annealing performed under hydrogen or argon atmosphere. We explore the effects of these treatments both on as grown and polished epilayers. Owing to an important initial surface roughness, the annealing has few impact on as grown films. On polished epilayers, a surface reorganization via the formation of a regular array of steps is evidenced. The proper effect of each gas on the surface reorganization is discussed.