Ultrathin insulating films on metal substrates are unique systems for using a scanning tunneling microscope (STM) to study the electron transport properties in the weak-coupling limit. The electronic decoupling provided by the films allows the direct imaging of the unperturbed molecular orbitals, as will be demonstrated in the case of individual pentacene molecules. The coupling between electronic states localized on the adsorbate and optical phonons in a polar insulator has two important implications: Peaks in conductance spectra resulting from resonant tunneling into electronic states of the molecules are significantly broadened by the presence of the insulator. Second, the ionic relaxations in a polar insulator may lead to an interesting charge bistability in atoms and molecules. STM-based molecular manipulation has been used to form a metallo-organic complex as well as to switch the position of the two hydrogen atoms in the inner cavity of single free-base naphthalocyanine molecules. © Schweizerische Chemische Gesellschaft.