Femtosecond laser is a perfect laser source for materials processing when high accuracy and small structure size are required. Due to the ultra short interaction time and the high peak power, the process is generally characterized by the absence of heat diffusion and, consequently molten layers. Various induced structures have been observed inside glasses after the femtosecond laser irradiation. Here, we report the refractive index change, space-selective valence state manipulation of active ions, nano-grating and precipitation control of nanoparticles by a femtosecond laser in glasses. The mechanisms of the observed phenomena were also discussed.