We present a study for large defects called protrusions that form during the hetero-epitaxy of SiC on Si. We focus first on surface morphology, size, three-dimensional shape and internal structure, and second on photoluminescence and Raman features. These defects have a peculiar 3D structure similar to inverted square pyramids with a vertex close to the SiC/Si interface. The size of the square and the height of the pyramid are both related to the thickness of the epi-layer and are spatially limited by the stacking faults in the {1 1 1} planes. The inner core of the defect consists of nano crystals twinned with respect to the substrate orientation. The defects demonstrate broad peculiar emission band at about 750 nm, while the usual photoluminescence signal from band recombination is at 520 nm. The SiC/Si interface is studied in order to investigate the seed of protrusion defect formation. We found that seeds …