A scanning thermal microscope (SThM) was used to measure the thermal conductivity of thin sputter-deposited films in the thickness range of 10 nm–10 μm. The SThM method is based on a heated tip that is scanned across the surface of a sample. The heat flowing into the sample is correlated to the local thermal conductivity of the sample. Issues like the contact force, the surface roughness of the sample, and tip degradation, which determine to a great extent the contact area between tip and surface, and thus the heat flow to the sample, are addressed in the paper. A calibration curve was measured from known reference materials to quantify the sample heat flow. This calibration was used to determine the effective thermal conductivity of samples. Further, the heat diffusion through a layered sample due to a surface heat source was analyzed with an analytical and numerical model. Measurements were performed with films of aluminum, ZnS–SiO2, and GeSbTe phase change material of variable thickness and sputter-deposited on substrates of glass, silicon, or polycarbonate. It is shown in the paper that the SThM is a suitable tool to visualize relative differences in thermal structure of nanometer resolution. Determination of the thermal conductivity of thin layers is possible for layers in the micrometer range. It is concluded that the SThM is not sensitive enough to measure accurately the thermal conductivity of thin films in the nanometer range. Suggestions for improvement of the SThM method are given.