We present a comparative study of the effects of low power reactive ion etching (RIE) on GaN and InN. This new, highly chemical, dry etching, using CF4 and Ar, has been developed for thin nitride films grown at low temperature in our laboratories. GaN films were grown by remote plasma enhanced-laser induced chemical vapor deposition and InN films were grown by radio-frequency RF reactive sputtering. Commercial GaN samples were also examined. Optical and electrical characteristics of the films are reported before and after removing 100 to 200 nm of the film surface by RIE. We have previously shown that the GaN films, although polycrystalline after growth, may be re-crystallized below the growth temperature. Removal of the surface oxide has been found to be imperative since a polycrystalline residue remains on the surface after re-crystallization.