In order to understand the physical processes associated with fs-laser waveguide writing in glass, the effects of the laser repetition rate, the material composition and feature size were studied. The resulting material changes were observed by collecting Raman and fluorescence spectra with a confocal microscope. The guiding behavior of the waveguides was evaluated by measuring near field laser coupling profiles in combination with white light microscopy. Waveguides and Bragg gratings were fabricated in fused silica using pulse repetition rates from 1 kHz to 1 MHz and a wide range of scan speeds and pulse energies. Two types of fluorescence were detected in fused silica, depending on the fabrication conditions. Fluorescence from self trapped exciton (E{prime}{sub {delta}}) defects, centered at 550 nm, were dominant for conditions with low total doses, such as using a 1 kHz laser with a scan speed of 20 {micro}m/s and pulse energies less than 1 {micro}J. For higher doses a broad fluorescence band, centered at 650 nm, associated with non-bridging oxygen hole center (NBOHC) defects was observed. Far fewer NBOHC defects were formed with the 1 MHz laser than with the kHz lasers possibly due to annealing of the defects during writing. We also observed an …