The region having the surface roughness has nitrogen vacancies, which serve as compensating donors for acceptors and therefore cannot achieve a sufficiently high p-type carrier concentration. In addition, the surface of the GaN-based material may be contaminated as a result of diffusion of impurities from the protective film or insufficient removal of the protective film. Such contamination may adversely affect the subsequent steps or the characteristics of completed devices.A first aspect of the innovations herein provides a method of manufacturing a nitride semiconductor device, including thermally treating a nitride semiconductor layer or removing a film formed on a front surface of the nitride semiconductor layer, and polishing the front surface of the nitride semiconductor layer after the thermally treating or the removing.