Sub-micron-structure machining on silicon substrate was studied by direct writing system of femtosecond laser with the central wavelength of 800 nm, pulse duration of 120 fs and repetition rate of 1 kHz. Three kinds of experiments were conducted: 1) the effect of photoresist on silicon; 2) machinability of different orientations of silicon; and 3) the size of micro-structure and the cross-section shape. Photoresist SU8 was coated onto silicon substrates in thicknesses of 100 μm. SU8 remained on the silicon substrate while the silicon under the machined SU8 was removed after laser machining. Orientations of (100), (110), and (111) silicon substrates were machined with the laser power of 60 μW and the scanning speed of 3 mm/min. Spike morphologies were observed on all three orientations of silicon substrates without obvious directional difference of these spikes on different silicon substrates. In addition, the ablation threshold energies were also similar. In the consideration of ablation energy, one numerical model of the machining parameters has been proposed to simulate the cross-section of the micro-structure. The predicted shape by simulation can fit the profile of the cross-section shape well. Sub-micron-structure machining on silicon substrate was studied by direct writing system of femtosecond laser with the central wavelength of 800 nm, pulse duration of 120 fs and repetition rate of 1 kHz. Three kinds of experiments were conducted: 1) the effect of 2) machinability of different orientations of silicon; and 3) the size of micro-structure and the cross-section shape. Photoresist SU8 was coated onto silicon substrates in thicknesses of 100 μm. SU8 remained on the silicon substrate while the (100), (110), and (111) silicon substrates were machined with the laser power of 60 μW and the scanning speed of 3 mm / min. Spike morphologies were observed on all three orientations of silicon substrates without obvious directional difference of these spikes on different silicon substrates. In addition, the ablation threshold energies were also similar. In the consideration of abla tion energy, one numerical model of the machining parameters has been proposed to simulate the cross-section of the micro-structure. The predicted shape by simulation can be the profile of the cross-section shape well.