Transparent materials are widely used in the fields of optic parts and bio industry. We have experiment to find out the characteristics of the micromachining inside transparent materials using femtosecond laser pulses. With its non-linear effects by very high peak intensity, filament (plasma channel) was formed by the cause of the self-focusing and the self-defocusing. Physical damage could be found when the intensity is high enough to give rise to the thermal stress or evaporation. At the vicinity of the power which makes the visible damage or modification, the structural modification occurs with the slow scanning speed. According to the polarization direction to the scanning direction, the filament quality is quite different. There is a good quality when the polarization direction is parallel to the scanning direction. For fine filament, we could suggest the conditions of the high numerical aperture lens, the short shift of focusing point, the low scanning speed and the low power below 20 mW. As the examples of optics parts, we fabricated the fresnel zone plate with the $225{mu}m$ diameter and Y-bend optical wave guide with the $5{mu}m$ width.