In the present experimental investigation we report a confocal micro-luminescence study of pure silica and borosilicate BK7 glass surfaces, irradiated with focused femtosecond laser pulses. For both glasses we detect several luminescence signals. In the case of the pure silica the emission of the NBOHC (Non-Bridging Oxygen Hole Centers) is detected in the non-ablated and non-densified regions, these defects are metastable (the signal almost disappears after one month from the irradiation). In ablated zones, under excitation at 633 nm, we detected at least an other metastable signal in time and a 550 nm emission, under excitation at 325 nm, which was previously detected in bulk when the refractive index decreases. In the case of BK7 a signal with a maximum at 565 nm is detected in non-ablated zones, this emission is present both in regions with increased and unchanged refractive indexes. In ablated zones we detected other signals in the range 650–700 nm, which exhibit relevant spectral modifications of the signal near the ablation conditions. The combined study and the 3-dimensional characterization of such emissions appear to be useful candidates for a deeper understanding of the ultrafast laser matter interaction, allowing a better characterization of the defect generation dependence as a function of laser fluence, number of pulses and wavelength.