High quality GaN films are grown on sapphire(0001) substrates by low pressure MOCVD using TMG and NH3 as source materials. Effects of surface nitridation and buffer layer thickness on the quality of over-grown GaN films are investigated. It is revealed by atomic force microscope (AFM) observations that surface roughness of the annealed buffer layers strongly depends on the nitridation time. Dislocation density and surface morphology of the high temperature GaN layer depend on the buffer layer thickness. It is found that sufficient surface nitridation of sapphire makes the buffer layer just prior to the high temperature growth very smooth, which is essential to obtain flat thick-GaN on it. It is also found that thickness of the buffer layer largely influences the dislocation density in the over-grown thick GaN. In order to obtain good surface morphology and low dislocation density at the same time, both nitridation time and buffer layer thickness must be optimized.