We have investigated the surface morphology of epitaxial layers etched by hydrogen annealing under the several conditions. The formations of the macro-steps were observed in the epitaxial layers on the 4H- and 6H-SiC(0001) Si faces with off angles grown by the vertical hot wall type CVD system under atmospheric pressure. The size of the steps was several hundreds run width and several ten nm height analyzed by atomic force microscopy. On the other hand, the surface roughness of the epitaxial layers grown under low-pressure atmosphere was less than 3 nm. The epitaxial films with macro-steps on 4H- and 6H-SiC (0001) Si faces were annealed in the atmosphere of hydrogen at high temperature region above 1400degreesC by the CVD system. The step heights of the macro-steps on the epitaxial layers drastically reduced after hydrogen annealing under low-pressure atmosphere.