The combination of vibrational spectroscopy and microscopy with the imaging, manipulation, and chemical modification capabilities of the scanning tunneling microscope (STM) has made it possible to probe surface chemistry with sub-Angstrom resolution. Direct visualization of the nature of the chemical bonds and their transformations at the single molecule level not only provides convincing evidences but also fundamental understandings of chemical processes. The STM junction is effectively a nanoreator in which the metallic tip and substrate work together to induce chemical transformations of individual molecules adsorbed either on the substrate or the tip. Many aspects of chemistry can be probed by the STM, including the rotational, vibrational, and translational motions, the conformational changes, the energy transfer, the electrical conductivity, the coupling of electrons to the nuclear motions, and the bond breaking and formation of individual molecules.