A system and method for permanently writing diffraction gratings in low phonon energy glass waveguides are shown. Ultrashort light pulses are generated and made to form two beams synchronously superimposed in the waveguide, therefore forming an interference pattern corresponding to the desired grating. The light pulses are focussed so that the light intensity in the waveguide exceeds a filamentation threshold. The exposure of the waveguide to these light pulses is controlled temporally and spatially in order to limit detrimental thermal effects induced by the high-intensity pulses in the glass medium of the waveguide.