Ill-nitride semiconductors are emerging as highly promising candidates for the fabrication of wide band-gap electronic and opto-electronic devices. Sapphire ((α-A12O3) is currently one of the primary substrates of choice for the growth of GaN despite a large lattice mismatch. Significant improvements in the quality of III-nitride layers have been demonstrated by exposure of the substrate to reactive nitrogen species followed by deposition of a low temperature AIN or GaN buffer layer. In this paper we present a study of the evolution of the surface topography and defect microstructure of nitrided α-A12O3 substrates and AIN buffer layers deposited by reactive molecular beam epitaxy (RMBE). Their influence on the morphology and properties of GaN layers is also discussed. Both nitridation time and AIN deposit thickness were varied systematically, at different temperatures and buffer growth rates. The microstructures were characterized using the atomic force microscope (AFM) and transmission electron microscope (TEM). Initial growth studies are ideally suited to in-situ experiments, and further investigations are also in progress using a unique UHV TEM with the facility for in-situ RMBE.