The growing energy demands for wearable electronic devices has shifted the attention of scientific community towards flexible thermoelectric materials and devices; the main goal being the enhancement of the thermoelectric and conducting properties of such systems, without sacrificing their flexibility. This paper reports the enhancement of the thermoelectric properties of flexible Poly(3,4-ethylenedioxythiophene), (PEDOT), films with acid (HCl) exposure. Relative high conductive, flexible and uniform PEDOT/polyurethane(PU) and (PEDOT)/polyvinylidene fluoride (PVDF) films were prepared, separately. The films were dipped into acid solution with the exposure time of 5, 10, and 15 min. The sheet resistance (Omega/sq), electrical conductivity (sigma), Seebeck coefficient (S) and thermoelectric power factor (sigma S-2) were measured for those systems. The thermoelectric behavior of both films was optimized with different exposure times in acid solution, while the thermoelectric properties of the PEDOT/PVDF films remained unchanged with this treatment. The Seebeck coefficient and thermoelectric power of PEDOT/PU enhanced from 9.01 to 12.6 mu V/K and from 7.4x10(-2) to 12.2x10(-2) mu W/mK(2), respectively for a 10 min exposure. The origin of this enhancement was tracked down to modifications in the surface morphology of the films, identified through AFM microscopy. The presented results indicate that acid treatment is a potential and promising approach to enhance the thermoelectric properties of PEDOT/PU films for flexible, conformable and low-cost TE applications.