Conducting polymers are prevalently used in organic and flexible electronics and energy conversion devices. While their thermo-physical properties are well characterized for different processing and doping conditions, very little is known about the effect of lengthscale, especially their thermal conductivity and thermal contact resistance of their interfaces with substrates. In this paper we develop an analytical model to capture the heat transfer in ultra-thin polyaniline thin films and their interfaces with other substrate materials. The model is demonstrated on 20-1000 nm thick 50% camphor-sulphonic acid doped polyaniline films patterned on silicon substrate using photolithography and reactive ion etching. The four-probe based technique allows simultaneous electrical and thermal characterization. Experimental results show a 500% and 200% increase in the in-plane thermal conductivity and electrical conductivity, respectively as the film thickness is increased from 20 nm to 1000 nm. These findings suggest up to 300% improvement in thermoelectric performance for 20 nm thick films when compared to the bulk. Such strong length-scale effects are observed to decay rapidly after 100 nm film thickness and can be attributed to the enhanced phonon scattering at the surface and interface boundaries at length-scales comparable to phonon mean free paths.