A sub-micron structure is fabricated in a transparent dielectric material by focusing femtosecond laser pulses into the dielectric to create a highly tapered modified zone with modified etch properties. The dielectric material is then selectively etched into the modified zone from the direction of the narrow end of the tapered zone so that as the selective etching proceeds longitudinally into the modified zone, the progressively increasing width of the modified zone compensates for lateral etching occurring closer to the narrow end so as to produce steep-walled holes. The unetched portion of the modified zone produced by translating the laser beam close to and parallel to the bottom surface of the dielectric can serve as an optical waveguide to collect light from or deliver light to the etched channel which can contain various biological, optical, or chemical materials for sensing applications.