A theoretical study of tip-induced desorption of benzene from a Si(100) surface is presented. The energetically forbidden process is triggered by inelastic resonance tunneling mediated by a cationic state of the substrate-adsorbate complex. Potential energy surfaces for the neutral and ionic states are computed within a cluster model. Quantum mechanical time-dependent wave packet calculations are used to explore the desorption dynamics. Extension of the scheme to study the response of different classes of organic adsorbates to tunneling current and to control of other surface reactions with a scanning tunneling microscope is discussed.