A nitrogen ion beam was used to etch the surface of CuInSe2 single crystals. This technique, applied to CuInSe2 for the first time, was studied with respect to surface damage production at various ion energies and was compared to commonly used argon ion sputtering. Raman scattering and atomic force microscopy were applied as characterization methods. We observed a stress induced redshift of the Raman mode for the argon etched samples which could be explained by tensile stress in the damaged layer. Nitrogen ion beam etching at an energy of 1000 eV causes a blue shift due to the increased lattice damage. Nitrogen ion beam etching at energies below 500 eV was found to produce the lowest degree of damage and the lowest surface roughness, as compared with mechanical polish or argon ion sputtering. Therefore, this method is suitable for dry etching and smoothing of CuInSe2.