In this work, the fabrication of optical waveguides embedded in fused silica (Suprasil1) and boro-aluminosilicate glass (Eagle2000) is demonstrated with femtosecond laser direct writing, as well as their suitability to be brought to the surface, through wet etching, for enhanced evanescent coupling with the external dielectric medium. Fused silica demonstrated to be inappropriate in this particular application, as the guiding region is at the bottom of the induced modification, creating a barrier between the guided mode and the substrate’s boundary. Furthermore, the existence of nanogratings meant that, upon contact of the top of the induced modification with the substrate’s boundary, the waveguide is quickly etched. Eagle2000 demonstrated to be superior to fused silica due to its characteristic modification cross-section and absence of nanogratings, which allowed the placement of the guiding region as close to the substrate’s surface as required. However, surface roughness arising from the creation of insoluble products in the HF solution was found. The addition of HCl to dissolve these products was implemented.