The integration of porous structures into microchannels is known to enable unique and useful separations both in electrophoresis and chromatography. Etched pillars and other nanostructures have received considerable interest in recent years as a platform for creating microchannels with pores tailored to specific applications. We present a versatile method for integration of three-dimensionally sculptured nano- and micro-structures into PDMS microchannels. Glancing angle deposition was used to fabricate nanostructures that were subsequently embedded in PDMS microchannels using a sacrificial resist process. With this technique, an assortment of structures made from a wide selection of materials can be integrated in PDMS microchannels; some examples of this versatility, including chiral and chevron nanostructures, are demonstrated. We also present a working device made using this process, separating 6/10/20 kbp and 10/48 kbp DNA mixtures in a DNA fractionator containing GLAD-deposited SiO(2) vertical posts as the separating medium. The separation mechanism was verified to resemble that found in prior fractionation devices, using total internal reflection fluorescence microscopy. GLAD fabrication enables insertion of three-dimensional structures into microchannels that cannot be fabricated with any existing techniques, and this versatility in structural design could facilitate new developments in on-chip separations.