Abstract We present results on a well known system, C 60 on Si(111)(7×7), which show that the scanning tunneling microscope (STM) is probing a single molecular orbital (MO). This MO, after comparison of experimental intramolecular structure with ab initio calculations, arises from the highest occupied MO (HOMO). The adsorbed molecules keep their relevant electronic identity but suffer a decrease in their icosahedral symmetry. The nature of the chemical bonding is proposed as being responsible for selecting one single MO in the imaging mechanisms. Our results represent an example of a strongly interacting system that can be interpreted with a great level of detail, overcoming substrate complexities.