The advent of ultrafast lasers has enabled micromachining schemes that cannot be achieved by other current techniques. Laser direct writing has emerged as one of the possible routes for fabrication of optical waveguides in transparent materials. In this thesis, the advantages and limitations of this technique are explored. Two extended-cavity ultrafast lasers were built and characterized as the laser sources for this study, with improved performance over existing systems. Waveguides are fabricated in oxide glass, chalcogenide glass, and polymers, these being the three major classes of materials for the telecommunication industry. Standard waveguide metrology is performed on the fabricated waveguides, including refractive index profiling and mode analysis. Furthermore, a finite-difference beam propagation method for wave propagation in 3D-waveguides is proposed. The photo-structural modifications underlying the changes in the material optical properties after exposure are investigated. The highly nonlinear processes of the light/matter interaction during the writing process are described using a free electron model. UV/visible absorption spectroscopy, photoluminescence spectroscopy and Raman spectroscopy are used to assess the changes occurring at the atomic level. Finally, the impact of laser direct writing on nonlinear waveguide applications is discussed.