The need for miniaturisation in devices in today's industries has led to a vast array of micromachining processes. Yet, micromachining of glass remains a great challenge due to the extreme brittleness and hardness of the material. With the development of the chirped pulse amplification (CPA) technique in the mid-1980s, powerful femtosecond (10-15 s) laser systems are now readily available in the market for carrying out micromachining on various materials. Femtosecond (fs) lasers have several advantages over their long pulse laser counterparts. First, the high intensity of femtosecond laser pulse will easily triggers the multiphoton absorption process to occur in transparent material enabling bulk modification within the transparent materials. Moreover, the ultrashort pulse duration (~100 fs) of a femtosecond laser enables energy to be dissipated before thermal diffusion occurs (~10 ps), thus collateral damages around the machined area is minimized. These unique properties have opened up new opportunities in using femtosecond lasers for carrying out micromachining and micro fabrication of glass and other transparent materials. Despite the ongoing work to study femtosecond laser-material interaction, practical use of femtosecond laser for industrial application can be still considered at the development stage as the beam interaction process is not well understood. New physical mechanism and phenomenon can arise when the machining is performed using different materials and conditions. Therefore, in this research, a femtosecond laser was used to carry ablation of transparent material in air using fused silica as a model optical material. The objective of this research is to gain a better understanding on the femtosecond laser irradiation effects on fused silica so that it can be applied to practical micromachining processes. These effects include ripple formation, change in crystal structures and surface morphologies as well as how the laser irradiated Abstract ii machined profiles respond to various laser parameters. Special attention was paid to characterize the laser irradiated morphologies and structures as well as studying phenomenon related to micromachining of fused silica. Major results and new findings are summarized as follows: Femtosecond laser induced periodic structures on fused silica were systematically studied by irradiating the surface using a wide range of laser processing parameters. It is found that two directional ripples having periods smaller than the laser wavelength can be formed on the surface of fused silica. It is demonstrated that the the origin of the coarse ripple is related to the ultrafast melting and solidification of fused silica and the fine ripple is a result of harmonica wave generation. It is also found that orientation and period of these ripple structures can be controlled experimentally by varying the beam polarization. It is further observed that the influence of the surface defect like scratches exert an even stronger influence on the ripple orientation than the beam polari...