We demonstrate mapping of electrical properties of heterojunctions cif a molecular semiconductor (copper phthalocyanine, CuPc) and a transparent conducting oxide (indium-tin oxide, ITO), in, 20-500 nm length scales, using a conductive-probe atomic force microscopy technique, scanning current spectroscopy (S(S). 5(5 maps are generated for CuPc/ITO heterojunctions as a function of ITO activation procedures and modification with variable chain length alkyl-phosphonic acids (Pk). We correlate differences in small length stale electrical properties with the performance of organic photovoltaic cells (OPVs) based on CuPc/C-60 heterojunctions, built on these same ITO substrates. SCS maps the "ohmicity" of ITO/CuPc heterojunctions, creating arrays of spatially resolved current-voltage (J-V) curves. Each J-V curve is fit with modified Mott-Gumey egressions, mapping a fitted exponent (gamma) where deviations from gamma = 2.0 suggest nonohmic behavior. ITO/CuPc/C-60/BCP/Al OPVs built on nonactivated ITO show mainly nonohmic SCS maps and dark J-V curves with increased series resistance (R-S), lowered fill-factors (FF), and diminished device performance, especially near the open-circuit voltage. Nearly optimal behavior is seen for OPVs built on oxygen-plasma-treated ITO contacts, which showed SCS maps comparable to heterojunctions of CuPc on clean Au. For ITO electrodes modified with Pk there is a strong correlation between PA chain length and the degree of ohmicity and uniformity of electrical response in ITO/CuPc heterojunctions. ITO electrodes modified with 6-8 carbon alkyl-PAs show uniform and nearly ohmic SCS maps, coupled with acceptable CuPc/C60OPV performance. ITO modified with C14. and C18 alkyl-PAs shows dramatic decreases In FF, increases in R-S, and greatly enhanced recombination losses.