GaN layers n sapphire substrates were prepared by using metal organic vapor phase epitaxy (MOVPE) combined with an in-situ H2 etching process for the purpose of later self-separation of thick GaN crystals produced by hydride vapor phase epitaxy (HVPE) on such substrates. The etching process results in deep pits and long voids that formed on the surface and along the lower interface between GaN and sapphire, respectively. The pits, which were investigated by SEM analysis, can be modified in their aspect ratio and density by controlling the etching parameters. Using a proper set of in-situ etching parameters, a seed layer with internal voids can be prepared, which is suitable for HVPE overgrowth and the self-separation process. The quality of the in-situ-etched seed GaN layer and overgrown GaN crystal were characterized by X-ray diffraction (XRD) and defect selective etching (DSE). With the aid of atomic force microscopy (AFM) in tapping mode, the interface morphology of the separated GaN crystal was analyzed. The crystal quality of the separated HVPE-GaN crystal is comparable to the crystal grown on untreated GaN MOVPE-seed, which did not separate from the sapphire substrate. The introduced technique to promote the crystal separation during the HVPE process has no obvious drawback on the quality of the grown GaN crystals. Using this technique, the self-separation occurs more gently due to a weakened interface between GaN/sapphire. The conventional separation from an untreated seed by pure thermomechanical action results in higher mechanical forces on the crystal and consequently much higher risk of crystal breakage.