We present the development and results of a new simple method for thermal conductivity characterization of thin films and thermoelectric structures using a scanning thermal microscope in pulsed current mode. The presented method does not allow measurement of absolute thermal conductivity of the studied system, but only relative to the Si substrate. We present the results of the method on the Si substrate/layer step boundary. The nano-layers of different thickness and different materials were prepared for the experiments by the pulsed laser deposition from hot-pressed targets.