In this paper, we present a novel approach developed in order to increase the reliability and accuracy of AFM investigation of morphological changes in a nanocomposite due to exposure to the media causing its degradation. By precise sample positioning and repetitive determination of the roughness changes at specific spots, we were able to create space-related degradation profiles. As the multi-step experiment based on exposure/scanning cycle was performed, we were able to observe a unique response of investigated samples revealing spatial inhomogeneity of the material. In order to present the measurement methodology, we used polystyrene samples containing various quantities of PC61BM nanofiller (0 %, 5 %, 10 % and 20 % of mass proportion), which was exposed to 370 nm UV radiation. Obtained data can be recognized as specific fingerprints of investigated materials. The solution based on creation and analysis of degradation profiles can be particularly useful for diagnostics of nanomaterials and nanocomposites to test their resistance to various conditions.