The widely used semiconducting polymers poly(3,4‐ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS) (PH1000), poly(3‐hexylthiophene‐2,5‐diyl) (P3HT), and Poly[[4,8‐bis[(2‐ethylhexyl)oxy]benzo[1,2‐b:4,5‐b′]dithiophene‐2,6‐diyl][3‐fluoro‐2‐[(2‐ethylhexyl)carbonyl]thieno[3,4‐b]thiophenediyl]] (PTB7) for organic photovoltaic (OPV) cells, are deposited on highly ordered pyrolytic graphite substrates and investigated by scanning tunneling microscopy (STM) under the liquid/solid interface technique. PEDOT:PSS film morphology shows an ellipsoidal shape of PEDOT surrounded by PSS with 4 nm size. STM images of P3HT reveal that films tend to form well‐defined crystalline domains with an average interchain distance around 1.41 nm and chain length ≈41 nm. PTB7 chains are self‐aggregated by using chlorobenzene as solvent; however, when using 1‐phenyloctane with 3% of 1,8‐diiodooctane, these chains show a worm‐like pattern with a distance of ≈2 nm between backbone chains and a chain length of ≈90 nm. For P3HT and PTB7 based OPVs, local J–V plots are determined from photoconductive atomic force microscopy (pc‐AFM) measurements and fitted with the modified Mott−Gurney equation, the reached parameters are correlated with those achieved from the macroscopic J–V graphs. Active films of OPVs cells based on PTB7 are also analyzed by using AFM phase imaging showing domains size of 80–120 nm. This current STM analysis can elucidate some new important insights on polymer film formation and morphology and therefore, their influence on the OPV performance.