Alignment of conjugated polymers such as regioregular poly(3-hexylthiophene-2,5-diyl) (rr-P3HT) is an effective means to enhance charge transport and thermoelectric properties of thin films doped with F4TCNQ. In this contribution, we investigate the impact of P3HT regioregularity (RR) on the alignment achieved in thin films by high temperature rubbing and the resulting thermoelectric properties in sequentially doped and aligned films. Structure and thermoelectric properties in doped P3HT thin films are investigated by a combination of transmission electron microscopy (electron diffraction), polarized UV-vis-NIR spectroscopy and thermoelectric measurements. Despite limited thermomechanical properties, rubbing at 165°C generates order and alignment in 71%RR P3HT (R71-P3HT) with a typical lamellar stacking of P3HT chains similar to that of the smectic-like phase of RR-P3HT. Order is further enhanced in aligned R71-P3HT films by doping with F4TCNQ. Intercalation of dopants in the ordered domains of R71-P3HT induces a reorganization of polythiophene backbones within individual -stacks with lattice parameter variations equivalent to those observed for RR-P3HT. Despite ordering induced by both rubbing at 165°C and doping, charge conductivity of oriented R71-P3HT in the chain direction remains 50-times below that of oriented RR-P3HT. The strong blue-shift of the polaronic bands in R71-P3HT versus RR-P3HT indicates that polarons are strongly localized in both ordered and amorphous zones of R71-P3HT, explaining the modest charge conductivity of 3-4 S/cm observed in the chain direction.