The products of photoreactions of conjugated organic molecules may be allowed by selection rules but not observed in solution reactions because of unfavorable reaction geometries. We have used defect sites in self-assembled alkanethiolate monolayers on gold surfaces to direct geometrically unfavorable photochemical reactions between individual organic molecules. High conductivity and stochastic switching of anthracene-terminated phenylethynylthiolates within alkanethiolate monolayers, as well as in situ photochemical transformations, have been observed and distinguished with the scanning tunneling microscope (STM). Ultraviolet light absorbed during imaging increases the apparent heights of excited molecules in STM images, a direct manifestation of probing electronically excited states.