In this paper, we show that simultaneous noncontact atomic force microscopy (nc-AFM) and scanning tunneling microscopy (STM) is a powerful tool for molecular discrimination on the Si(111)-7 × 7 surface, even at room temperature. Using density functional theory modeling, we justify this approach and show that the force response allows us to distinguish straightforwardly between molecular adsorbates and common defects, such as vacancies. Finally, we prove that STM/nc-AFM method is able to determine attachment sites of molecules deposited on semiconductor surface at room temperature.