We present novel results obtained in the fabrication of high-aspect ratio micro-fluidic microstructures chemically etched from fused silica substrates locally exposed to femtosecond laser radiation. A volume sampling method to generate three-dimensional patterns is proposed and a systematic SEM-based analysis of the microstructure is presented. The results obtained gives new insights toward a better understanding of the femtosecond laser interaction with fused silica glass (a-SiO2).