GaN films have been grown on SiC substrates with an AlN nucleation layer by using a metal organic chemical vapor deposition technique. Micro-cracking of the GaN films has been observed in some of the grown samples. In order to investigate the micro-cracking and microstructure, the samples have been studied using various characterization techniques such as optical microscopy, atomic force microscopy, Raman spectroscopy, scanning electron microscopy and transmission electron microscopy (TEM). The surface morphology of the AlN nucleation layer is related to the stress evolution in subsequent overgrown GaN epilayers. It is determined via TEM evidence that, if the AlN nucleation layer has a rough surface morphology, this leads to tensile stresses in the GaN films, which finally results in cracking. Raman spectroscopy results also suggest this, by showing the existence of considerable tensile residual stress in the AlN nucleation layer. Based on these various observations and results, conclusions or propositions relating to the microstructure are presented.