Images of the surface were obtained using AC-mode AFM exciting higher-order resonance frequencies of a standard silicon probe, a promising technique for acquiring real-space images of organic-based thin films with nanoscale and even submolecular resolution. We provide firm evidence of the nanoscale organization of the P3HT polymer and of the P3HT:PCBM stoichiometric mixtures at the surface–air interface of the BHJ architecture. Our study shows the characteristic periodicity of the regioregular P3HT identified in the nanoscale domain areas with submolecular resolution. Such areas are then distorted in place when adding different quantities of PCBM forming stoichiometric mixtures. When the samples were exposed to ambient light, the morphologies were very different, and submolecular resolution was not achieved. This approach is shown to provide a precise view of the active layer’s nanostructure and will be useful for studies of other materials as a function of various parameters, with particular attention to the role of the acceptor in tuning morphology for understanding optimum performance in organic photovoltaic devices.