GaN-based bipolar transistors are good candidates for applications in RF power amplifiers. In contrast to more common AlGaN/GaN high electron mobility transistors (HEMTs), GaN based bipolar transistors have not drawn much attention because of the difficulties in good p-type material and ohmic contact. Most of the problems associated with p-type quality and contact come from growth and etch damage during fabrication. In this work, a low damage etching technique with an undercut profile was developed to solve the problems associated with p-type ohmic contact quality and to realize the self-aligned GaN bipolar transistor fabrication. The etching process consists of bias-assisted photoenhanced electrochemical oxidation of GaN in deionized water (BPECO/DI) and its subsequent etching in diluted acid solution. By this technique, we demonstrated good Schottky contacts on samples etched more than 100 nm and p/n doping selective etching was shown. Furthermore the most critical point for self-aligned fabrication is undercut profile and it was also obtained by BPECO/DI etching. Hence this technique is ideal for fabrication of self-aligned bipolar transistors. There are some problems during fabrication of self-aligned bipolar transistor. First, due to the impossibility of activation annealing after emitter etch, activation annealing had to be done at the beginning where emitter layer is on the base and this was a problem for Mg activation. More importantly, there were still uncertainties with BPECO/DI etching like roughening up the etched surface, low etch rate for npn structures and disturbing the material uniformity near the surface. In this work, it was shown that BPECO/DI etching is a very efficient tool that provided low damage etching of GaN and enabled the self aligned RF bipolar transistor structures. It was found that self aligned base-emitter junctions were successfully formed and the BPECO/DI etching was almost stopped at top of the base layer. Self-aligned bipolar transistors were fabricated and their base-emitter and base-collector junctions were measured. The results obtained in this work demonstrated that BPECO/DI etching can bring solutions to the lack of low damage etching and the impossibility of self-aligned base contact in fabrication of today’s GaN based bipolar transistors.