We report the relationship between the initial glass composition and the resulting microstructural changes after direct femtosecond laser waveguide writing with a 1 kHz repetition rate Ti:sapphire laser system. A zinc polyphosphate glass composition with an oxygen to phosphorus ratio of 3.25 has demonstrated positive refractive index changes induced inside the focal volume of a focusing microscope objective for laser pulse energies that can achieve intensities above the modification threshold. The permanent photo-induced changes can be used for direct fabrication of optical waveguides using single scan writing techniques. Changes to the localized glass network structure that produce positive changes in the refractive index of zinc phosphate glasses upon femtosecond laser irradiation have been studied using scanning confocal micro-Raman and fluorescence spectroscopy. © 2011 Optical Society of America.