At energy level below the ablation threshold, femtosecond-laser irradiation of Fused Silica (a-SiO2) can induce significant changes in the material properties: the refractive index and the chemical etching susceptibility can both be significantly increased. Using these effects one can scan a femtosecond laser beam through the substrate volume in order to create three-dimensional patterns with tailored material properties. Based on this approach, optical elements such as waveguides can be embedded in glass substrates. The elements can be provided with various functionalities such as for instance fluidic channels or micro-mechanical elements. In this paper, we show that femtosecond laser irradiation applied to Fused Silica (a-SiO2) defines a novel technology platform for highly integrated all-optical microsystems. In contrast to the common approaches that rely on combining materials to achieve particular functions, our technology utilizes a single piece of material, whose properties are locally functionalized through femtosecond laser irradiation. This leads to a new micro-systems design paradigm, whose potential is illustrated with a few examples in this paper.