We have developed a process using electron beam lithography and reactive ion etching for the high resolution pattern transfer of GaN. 150 nm dots have been fabricated in GaN successfully. Photoluminescence, scanning electron microscopy, and x-ray photoelectron spectroscopy have been employed to compare the damage inflicted on the GaN surfaces after SF 6 and Ar plasma exposures. Near-band-edge luminescence analysis indicates the existence of a higher concentration of donors on the top 100 nm of the GaN surface after Ar as supposed to SF 6 plasma exposure. An order of magnitude decrease in the ratio of the yellow to the band-edge luminescence intensity is found in the samples subjected to lower ion energies. Formation of pits is observed on the substrate surfaces after plasma treatment. Nitrogen deficient surfaces limited to the top few monolayers, as well as defect propagation down to 100 nm, exist in our plasma exposed GaN samples.