Fabrication of three-dimensional microstructures and microdevices based on femtosecond laser modification and machining of transparent materials has attracted much attention. Microfabrication techniques and their applications are introduced, including femtosecond laser induced refractive index change for fabrication of optical waveguides, gratings and couplers;microexplosion inside materials for three-dimensional bit-oriented storage and other dot-arrayed structures;interface ablation for drilling, cutting and etching;two-photon polymerization for microlens, photonic cryatals and diffractive optical elements.