Femtosecond laser irradiation has various noticeable effects on fused silica. It can locally increase the index of refraction and modify the material chemical selectivity. Regions that have been exposed to the laser are etched hundred fold faster than unexposed regions. These effects are of practical importance from an application point-of-view and open new opportunities for the development of integrated photonics devices that combine structural and optical functions. Various observations reported in the literature indicate that those effects are potentially related to a combination of both structural changes and the presence of internal stress. In this paper, we present further investigations on the effect of femtosecond laser irradiation on fused silica substrate (a-SiO2). In particular, we use nanoindentation and holography- based birefringence measurements, coupled with direct SEM observations on chemically etched specimens to characterize the effect of various laser parameters such as power, scanning speed and irradiation pattern. We show evidence of an interface between two different etching regimes that may be related to the presence of two different material phases induced by the laser irradiation.