This paper examines the capability of the HarmoniX Atomic Force Microscopy (AFM) technique to draw accurate and reliable micromechanical characterization of complex polymer morphologies generally found in conventional thermoplastic polymers. To that purpose, injection molded polypropylene samples, containing representative morphologies, have been characterized by HarmoniX AFM. Mapping and distributions of mechanical properties of the samples surface are determined and analyzed. Effects of sample preparation and test conditions are also analyzed. Finally, the AFM determination of surface elastic moduli has been compared with that obtained by indentation tests, finding good agreement among the results.