Selective area thermal etching (SATE) of gallium nitride is a simple subtractive process for creating novel device architectures and improving the structural and optical quality of III-nitride-based devices. In contrast to plasma etching, it allows, for example, the creation of enclosed features with extremely high aspect ratios without introducing ion-related etch damage. We report how SATE can create uniform and organized GaN nanohole arrays from c-plane and (11-22) semi-polar GaN in a conventional MOVPE reactor. The morphology, etching anisotropy and etch depth of the nanoholes were investigated by scanning electron microscopy for a broad range of etching parameters, including the temperature, the pressure, the NH3 flow rate and the carrier gas mixture. The supply of NH3 during SATE plays a crucial role in obtaining a highly anisotropic thermal etching process with the formation of hexagonal non-polar-faceted nanoholes. Changing other parameters affects the formation, or not, of non-polar sidewalls, the uniformity of the nanohole diameter, and the etch rate, which reaches 6 µm per hour. Finally, the paper discusses the SATE mechanism within a MOVPE environment, which can be applied to other mask configurations, such as dots, rings or lines, along with other crystallographic orientations.