Various examples of methods and systems related to nanofibrous microstructures including carbon nanofibrous microelectrode arrays are provided. In one example, a method includes electrospinning photosensitive nanofibers on a patterned substrate; immersing the photosensitive nanofibers in a refractive index matching medium; and exposing the immersed photosensitive nanofibers to ultraviolet (UV) light through the patterned substrate or through a front side photomask. In another example, a microelectrode array includes a carbon thin film (CTF) trace pattern including a plurality of CTF electrode pads; and a plurality of carbon nanofiber (CNF) pillars disposed on the plurality of CTF electrode pads.