Development of devices based on the wide gap semiconductor gallium nitride (GaN) requires the realization of reliable, high fidelity, low damage pattern transfer processes. In this work, GaN thin films grown by OMVPE have been subjected to both chlorine- and methane/hydrogen-based etch chemistries in an electron cyclotron resonance microwave plasma reactive ion etching system. Both n-type and semi-insulating thin films have been utilized to examine the effect of these etch processes on the electronic properties of the materials. The methane/hydrogen-based etch system (CH4/H2/Ar) induced considerable changes in the electrical properties of both n-type and semi-insulating films, causing the former to become more insulating and the latter to become conducting. In both cases, the original electrical properties were recoverable after a short, high temperature anneal. In the chlorine-based etching system (Cl2), no changes in the electrical properties were observed and etch rates five times greater than in the methane/hydrogen-based system were achieved. Proposed mechanisms responsible for the observed behavior will be discussed. These results show that pattern transfer processes based in chlorine etch chemistries are more suitable for the generation of high performance GaN devices.