We describe an innovative mode for localizing surface molecules. In this methodology, individual C60 impacts at 50 keV are localized using an electron emission microscope, EEM, synchronized with a time-of-flight mass spectrometer for the detection of the concurrently emitted secondary ions. The instrumentation and methodologies for generating ion maps are presented. The performance of the localization scheme depends on the characteristics of the electron emission, those of the EEM and of the software solutions for image analysis. Using 50 keV C60 projectiles, analyte specific maps and maps of co-emitted species have been obtained. The individual impact sites were localized within 1-2 μm. A distinctive feature of recording individual impacts is the ability to identify co-emitted ions which originate from molecules co-located within ∼10 nm.