Photo generated charge transport in bulk heterojunction (BHJ) solar cells is strongly dependent on the active layer nanomorphology resulting from phase segregation and connectivity of the donor and acceptor regions. Scanning probe-based techniques and in particular conductive-tip atomic force microscopy (CAFM) in dark and under illumination have provided useful information on the role of nanomorphology and charge transport in these blended systems; however, results and interpretations of the data are often complicated or poorly understood due to the complex nature of the BHJ/tip contact. Here, we provide insight on the nanoscale photocurrent response from BHJs based on poly(3-hexylthiophene) and Phenyl-C61-butyric acid methyl ester (P3HT:PCBM) by using the local probing capabilities of an atomic force microscope (AFM) to make contact with arrays of metallic nanodots on the film surface eliminating tip-contact issues. We observe significant inhomogeneity in the measured photocurrent from these nanodevices on the scale of a few hundred nanometers without a direct correlation to topographical features. We explore the current-voltage characteristics of these nanodots in dark and under light as a function of the contact area to study the extent of the photocurrent variation and blending in the film. Finally, we compare these results with conventional CAFM on the active layer using both high and low work function tips and discuss the similarities and the differences and the evolution of photocurrent scans as a function of the substrate bias.