Methods for modifying the interface of optical substrates. To achieve desirable optical properties, surface defects need to be removed from the interface layer. In one example, a substrate is exposed to an ion beam then a high temperature bake or laser annealing to correct the interface layer. In another example, a high energy ion beam can be used to remove the interface layer then a new interface layer can be added during a high temperature bake or laser annealing with a protective layer added last. If not removed surface defects in the interface layer may absorb a percentage of light in a single interaction. In a waveguide, light may bounce ten to hundreds of times inside a substrate causing significant light loss. Therefore, removing the surface defects significantly increases waveguide efficiency.