Redox doping is widely used to transform polymer semiconductors such as regioregular poly(3-hexylthiophene) into conducting polymers. Strong acceptor molecules such as F 6 TCNNQ and F 4 TCNQ have been used for sequential doping of aligned P3HT films to produce films with enhanced thermoelectric properties along the chain direction. This study uses Polarized UV-vis-NIR spectroscopy and electron diffraction to clarify the way dopant molecules are introduced in the crystals of P3HT. A structural model is obtained for F 6 TCNNQ-doped P3HT (P-1 symmetry, a=18.8 Å, b=8.95 Å, c=7.75Å, =107.6°, =101.5° and =89.3°). The proposed structure is consistent with the electron diffraction pattern and polarized UV-vis-NIR results. The model predicts intercalation of one dopant per four thiophene monomers, reduced -stacking distance and expanded unit cell along alkyl side chains. Both TEM and polarized absorption spectroscopy demonstrate that F 6 TCNNQ molecules are better ordered than F 4 TCNQ in the P3HT crystals, leading to improved charge conductivities reaching 500 S/cm with thermoelectric power factors close to 80 W m -1 K -2 .