Photoinduced trans-cis isomerization studies of stilbene molecules in the gas phase have led to a precise understanding of the corresponding molecular dynamics. Yet, when such molecules are adsorbed on surfaces, these reactions are expected to be strongly modified as compared to what is know in the gas phase. In this work, a low temperature (5 K) scanning tunneling microscope (STM) is used to image the trans-stilbene molecules deposited on a Si(100)-2x1 surface at 12 K. trans-Stilbene undergoes conformational changes during the adsorption process such that four different stilbene conformers are observed: trans-stilbene (TS), cis-stilbene (CS), and two new conformers I-1 and I-2. Furthermore, electronic excitation of individual stilbene molecules, by means of tunnel electrons, is shown to activate specific reversible molecular surface isomerization (TS <-> I-1 and CS <-> I-2) combined with diffusion across the surface. Calculated STM topographies, using the tight binding method, indicate that the CS and TS molecules are physisorbed. The molecular conformations of the surface isomers I-1 and I-2 are suggested to be analogous to transient states conformations of the stilbene molecule when stabilized by the silicon surface. The measurements of the molecular surface isomerization and diffusion reaction yields are used to build a qualitative potential energy surface of the various stilbene reactions. The molecular surface-isomerization dynamics is shown to be influenced by the type of dopant (n or p). This is related to surface charging, which reveals modifications in the stilbene ionization potential.