Abstract: A photonic fabrication apparatus for making a waveguide in a glass substrate having a metal mask defining a region for the waveguide. The apparatus includes a molten salt, and a sacrificial anodic reaction material, in contact with the salt, that reacts with one or more contaminants in the salt. Also described is a salt-melt ion-exchange system having a chemical secondary reaction in the salt melt to prevent or reduce any primary reaction at or near the waveguide that would otherwise roughen sides of the waveguide and/or the surface over the waveguide.