A novel method for the direct fabrication of arrays of micropatterned polymeric and carbon nanofiber structures on any substrate is developed. First SU-8, an epoxy-based negative photoresist, is electrospun under optimized conditions to produce a layer of polymeric nanofibers. Next, this nanofibrous mat is micropatterned using photolithography, and finally, pyrolysis produces ordered arrays of microdomains containing carbon nanofibers. The nanotextured surfaces of carbon nanofibers are shown to be very hydrophobic (water contact angle ∼130°). Micropatterning thus generates a substantial wettability contrast of nanofiber domains with intervening micropatches of very hydrophilic carbon (∼20°) or silicon substrates. © 2010 American Chemical Society.