Using high surface area nanostructured electrodes in organic photovoltaic (OPV) devices is a route to enhanced power conversion efficiency. In this paper, indium tin oxide (ITO) and hybrid ITO/SiO(2) nanopillars are employed as three-dimensional high surface area transparent electrodes in OPVs. The nanopillar arrays are fabricated via glancing angle deposition (GLAD) and electrochemically modified with nanofibrous PEDOT:PSS (poly(3,4-ethylenedioxythiophene):poly(p-styrenesulfonate)). The structures are found to have increased surface area as characterized by porosimetry. When applied as anodes in polymer/fullerene OPVs (architecture: commercial ITO/GLAD ITO/PEDOT:PSS/P3HT:PCBM/Al, where P3HT is 2,5-diyl-poly(3-hexylthiophene) and PCBM is [6,6]-phenyl-C(61)-butyric acid methyl ester), the air-processed solar cells incorporating high surface area, PEDOT:PSS-modified ITO nanoelectrode arrays operate with improved performance relative to devices processed identically on unstructured, commercial ITO substrates. The resulting power conversion efficiency is 2.2% which is a third greater than for devices prepared on commercial ITO. To further refine the structure, insulating SiO(2) caps are added above the GLAD ITO nanopillars to produce a hybrid ITO/SiO(2) nanoelectrode. OPV devices based on this system show reduced electrical shorting and series resistance, and as a consequence, a further improved power conversion efficiency of 2.5% is recorded.