Periodic microripple structures were formed on the sample surface after micromachining on Cr-coated glass and fused silica by trains of femtosecond laser pulses from the oscillator. The heights of these microripple structures varied from 10 nm to 300 nm by increasing the laser power and saturated at a higher laser power. The morphology, sizes and heights of theses microstructures are depended on the irradiation fluences and parameters of the femtosecond laser pulses. Chemical methods proved that the microripple structures are composed of not chromium material but the substrate material of glass or fused silica. Furthmore, two kinds of grating with different periods and linewidths were fabricated by selecting the laser power and micromachining speed properly, which indicated the good micromachining performances of the femtosecond laser oscillator.