The results of a comparative study of the defect microstructures at different regions in epitaxial, monocrystalline GaN structures grown selectively within windows in and laterally over SiO2 masks deposited on GaN/AlN/6H-SiC heterostructures are presented. The defects in the GaN grown within the SiO2 windows were predominantly threading dislocations of mostly mixed character with Burgers vector b = 1/3(1 1 (2) over bar 3) and edge dislocations with b = 1/3(1 1 (2) over bar 0) with a density range of 10(9)-10(10)cm(-2) as determined using transmission electron microscopy (TEM). The regions of lateral epitaxial overgrowth (LEO-GaN) contained short dislocation segments parallel to the interfacial planes, which were usually aligned parallel or nearly parallel to the (1 (1) over bar 0 0) or (1 1 (2) over bar 0) directions and with densities of less than or equal to 10(6) cm(-2) Specific morphologies exhibited by the LEO-GaN were determined to be associated with the mechanism of stress relaxation. Finite element analysis of these complex heterostructures showed that the accommodation of the mismatches in the coefficients of thermal expansion among the different phases in the heterostructures was manifest in the formation of the curved surfaces observed in cross-sectional TEM.