Silicon thin films have great potential as chip-integrated Peltier micro-coolers and thermoelectric power generators due to their industry compatibility and cost effectiveness. Improving the thermoelectric figure of merit, zT, and therefore the device efficiency can be achieved by increasing the power factor while decreasing the thermal conductivity. In this work, we study single crystalline silicon thin films with patterned nano-holes with sizes comparable to the phonon mean free path to suppress thermal conductivity. The holey silicon thin films are then surface doped with organic molecules F4TCNQ to create a three-dimensional modulation doping scheme. As the dopants are outside the host material, there is less impurity scattering, which improves carrier mobility and the overall power factor. We fabricate silicon thin films with periodic arrays of nano-sized holes, with a fixed pitch size of 300 nm. By changing the hole diameters, we vary the neck size from 169 nm to 22 nm. The in-plane thermal conductivity, measured using the heat diffusion imaging method, demonstrates an order of magnitude reduction compared to bulk silicon and a change from 26 Wm−1K−1 to 5 Wm−1K−1 at room temperature. The films with large hole diameters allow space for the relatively large F4TCNQ molecules and hence effective surface doping, which is evident by orders of magnitude improvement in the electrical conductivity and power factor.