It depends on which direction you wish to have the measurement. In the plane of the film, or through the thickness of the film? Regardless, there are no really easy methods. TDTR (time domain thermal reflectance) is straightforward but requires a very special setup. Otherwise, you will likely need to be able to thermally isolate the film from the substrate, which requires fabrication, etc. Good luck.
Now if I want to calculate the thermal conductivity of isolated thin film by glass substrate , and to measure the thermal conductivity in plane to 50 nanometer thickness and ( 200*200) nm^2 area.