A new method for evaluating the thermal properties of the films and detecting fabrication failures has been provided. Moreover, this article studies the characterization of biaxially oriented polypropylene films (BOPP) using the Microthermal Analizer (muTA 2990). This instrument combines high-resolution imaging capabilities of the atomic force microscopy (AFM) with physical characterization by thermal analysis. In the first part of the work, topographic images of the film surfaces were obtained by AFM. They showed that the fabrication process and additives to the films caused differences in the sample topography. In the second part, the thermal conductivity images of multilayer films were obtained by thermal analysis mode. The thickness of each layer was determined for several BOPP films, based on the thermal conductivity signal registered by muTA 2990. Finally, it has been proven that this new technique is valid for detection of thermal transitions in polymer samples. Thus, melting points and glass transitions were measured in the samples with thermal probe.