We report on the microstructuring of Nd:YAG crystals by direct proton-beam writing. Buried channel waveguides have been fabricated with full spatial control by the combined variation of crystal position and proton energy. The fluorescence images of the obtained structures have been used to evaluate the potential application of the fabricated structures for laser gain as well as to elucidate the mechanism at the basis of the refractive index increment induced at the end of the proton path. We have concluded that this increment is very likely a local enhancement in the electronic polarizability caused by nuclear collisions. © 2010 Optical Society of America.