The surface of 4H-SiC and 6H-SiC substrates, both processed with and without LPE to fill micropipe defects, has been investigated by transmission electron microscopy and x-ray topography techniques to determine the status of existing unfilled and filled micropipes. Unfilled micropipes are hollow-core pure screw dislocations extending along the [0001] direction of the hexagonal crystal. Substrates processed with the micropipe filling process appear to possess a lower density of micropipes than those fabricated without the micropipe filling process. Initial homoepitaxial growth of SiC inside the micropipe channels by LPE techniques appears to fill or partially fill the micropipe core but likely retain screw dislocations in closed core form. Subsequent LPE layer growth on these modified substrates keeps the continuity of close packed atomic stacking of the original substrate with closed-core screw dislocations from the filled micropipes transforming into either a nano-pore extending mostly along the [000 1] direction of the substrate, or a grain boundary dislocation. Homoepitaxial growth into micropipe channels is suggested to produce an incoherent interface between the substrate and filled material and produces misfit dislocations in the subsequent LPE layer. CVD SiC epitaxially grown on these materials exhibited a smooth interface with the LPE SiC layer and greatly reduced the step-bunching present in the LPE layer.