Understanding nanoscale morphological and electrical properties of molecular-doped organic semiconductor (OSC) thin films is critical to modulate their bulk properties. In OSC, doping is achieved by blending the hosts with molecular dopants. Consequently, the nanostructures of the doped films are strongly dependent on processing conditions, such as dopant concentration and temperature. The ability to visually map out this nanostructure is essential but has not been reported yet. In this study, we manage to directly visualize the distribution of doping sites in the P3HT:F4TCNQ thin films at low dopant concentration by conducting atomic force microscopy (c-AFM). The dispersed dopant sites in the doped films, which cannot be easily visualized by other techniques, appear as high-current spots in nanoscale c-AFM images. At high dopant concentration, c-AFM current vastly enhances and becomes evenly distributed throughout the film. It is consistent with the reported hypothesis that, F4TCNQ molecules separately stay in amorphous regime of P3HT films at low concentration, whereas at higher concentration, they incorporate into the crystalline regime of P3HT films, resulting in the formation of new crystalline domains. We also demonstrate that c-AFM provides a facile way to monitor the changes of morphology and doping efficiency as a function of processing temperatures. Our results here not only provide an insightful depiction of the nanoscale structure in molecular-doped thin films, but also prove that c-AFM is a powerful and facile tool for analyzing dopant distributions and phase separation.