Effect of surface irregularities on defect nucleation and development in thick epitaxial layers of 4H-SiC has been investigated. It has been shown that during growth extended defects may undergo transformation and thus stacking faults can be formed, which is favored in thicker layers (e.g. 50mum). Network of misfit dislocations appears if the initial surface has a certain critical roughness and a lower surface energy. Evidence has been presented that well ordered graphite layer might form on the substrates during the preheating stage prior to growth via sublimation.