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The authors demonstrate the fabrication of multiscale electrodes (with lateral dimensions ranging from 10 μm to a few hundred of nanometers) on organic donor–acceptor photovoltaic thin films by mean of nanostencil lithography. The experimental setup allows the realization and in situ investigation of structures by combining nanostencil and atomic force microscopy (AFM) capabilities based on the use of tuning forks. Qplus AFM sensors with tungsten etched tips were used for near field imaging, and as microprobes to contact the deposited electrodes. The photovoltaic behavior was characterized by mean of current–voltage measurements in dark and under selective illumination. The influence of the electrode geometry on the electrical parameters is analyzed and the effect of in situ annealing is discussed in view of frequency modulation AFM images of the active layer surface morphology. This illustrates the powerfulness of nanostencil combined with Qplus AFM for local investigations of organic photovoltaic materials and in situ fabrication of devices.