Abstract Cathodoluminescence spectra provide an effective means of recording the changes in surface quality of Nd:YAG crystals resulting from polishing or ion beam amorphization. There are spectral shifts in wavelength and changes in intensity linked to imperfections caused by surface preparation such as polishing, chemical etching or by ion beam bombardment. The wavelength shifts between the Nd ion spectra from surface damaged and bulk material can approach 10 nm. Cathodoluminescence intensity is suppressed by factors of >3 as the result of polishing damage, and by up to 1000 times after amorphization of the surface. The depth profiles of these changes and their wider implications for losses in surface waveguide structures, waveguide lasers and cathodoluminescence imaging are discussed.