Glass drilling and welding applications realized with the help of femtosecond lasers attract industrial attention , however, desired tasks may require systems employing high numerical aperture (NA) focusing conditions, low repetition rate lasers and complex fast motion translation stages. Due to the sensitivity of such systems, slight instabilities in parameter values can lead to crack formations, severe fabrication rate decrement and poor quality overall results. A microfabrication system lacking the stated disadvantages was constructed and demonstrated in this report. An f-theta lens was used in combination with a galvanometric scanner, in addition, a water pumping system that enables formation of water films of variable thickness in real time on the samples. Water acts as a medium for filament formation, which in turn decreases the focal spot diameter and increases fluence and axial focal length . This article demonstrates the application of a femtosecond (280fs) laser towards two different micromachining techniques: rapid cutting and welding of transparent materials. Filament formation in water gives rise to strong ablation at the surface of the sample, moreover, the water, surrounding the ablated area, adds increased cooling and protection from cracking. The constructed microfabrication system is capable of drilling holes in thick soda-lime and hardened glasses. The fabrication time varies depending on the diameter of the hole and spans from a few to several hundred seconds. Moreover, complex-shape fabrication was demonstrated. Filament formation at the interface of two glass samples was also used for welding applications. By varying repetition rate, scanning speed and focal position optimal conditions for strong glass welding via filamentation were determined.