We examined the feasibility of making various microscopic modifications in glasses by ultra-short pulses. It was confirmed that permanent refractive index changes, photo- reduction of samarium ions, the phenomenon of long-lasting phosphorescence, and creation of microcrystals with second- order nonlinear optical functions can be produced with a femtosecond pulse laser only in selective internal areas in glasses. By using a femtosecond laser with a high repetition rate, permanent optical waveguides can be successfully written in various glasses, where refractive index changes are continuously induced along a path traversed by focal point. We also confirmed that only rare earth ions of the core region in the waveguides are reduced by the laser irradiation.