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 NH 3 flow rate and the carrier gas mixture. The supply of NH 3 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. Nanostructures are continuously drawing the attention of the III-nitride community for their success in improving light emitting devices 1-4 and their use for emerging applications such as water splitting 5 , single photon sources 6 , piezoelectric nanogenerators 7 or solar light harvesting 8. Among the different geometries available, arrays of nanoholes, in the form of a porous or two-dimensional photonic crystal (2D PhC) layer, have been widely investigated. On one side, a porous layer can provide a change in refractive index 9,10 , an increased surface area resulting in both higher sensitivity 11 and larger photocurrent 12,13 , a more efficient light extraction due to enhanced scattering 14,15 , and improved crystal quality by reducing strain and dislocation density 16-19. On the other side, a 2D PhC layer allows one to enhance the IQE thanks to the Purcell effect, increase the light extraction efficiency and improve/control the directionality of III-nitride based light emitting diodes (LED) 20-23. As such, networks of nanoholes have been used in several applications such as distributed Bragg reflectors 10 , sensors 11 , hydrogen generation 12,13 , LEDs 14,22,23 , free-standing GaN films 17 , and energy storage 18,19. The fabrication of nanohole arrays is usually achieved from a III-nitride layer or an LED structure via a subtractive process or what is called a top-down approach. Porous layers are generally obtained from GaN layers by various techniques, such as electrochemical etching 9,11,14,16 , photo-electrochemical etching 12,13 , metal assisted chemical etching 24,25 , and high temperature annealing with 26 , or without, a catalyst 15,17-19,27,28. Although the depth of the pores can reach a few microns 13,17-19,24,2...