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Organic thermoelectrics offer the potential to deliver flexible, low-cost devices that can directly convert heat to electricity. Previous studies have reported high conductivity and thermoelectric power factor in the conjugated polymer poly[2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene] (PBTTT). Here, we investigate the thermoelectric properties of PBTTT films in which the polymer chains were aligned uniaxially by mechanical rubbing, and the films were doped by a recently developed ion exchange technique that provides a choice over the counterions incorporated into the film, allowing for more optimized morphology and better stability than conventional charge transfer doping. To optimize the polymer alignment process, we took advantage of two Design of Experiment (DOE) techniques: regular two-level factorial design and central composite design. Rubbing temperature Trub and post-alignment annealing temperature Tanneal were the two factors that were most strongly correlated with conductivity. We were able to achieve high polymer alignment with a dichroic ratio >15 and high electrical conductivities of up to 4345 S/cm for transport parallel to the polymer chains, demonstrating that the ion exchange method can achieve conductivities comparable/higher than conventional charge transfer doping. While the conductivity of aligned films increased by a factor of 4 compared to unaligned films, the Seebeck coefficient (S) remained nearly unchanged. The combination of DOE methodology, high-temperature rubbing, and ion exchange doping provides a systematic, controllable strategy to tune structure–thermoelectric property relationships in semiconducting polymers.