The mechanisms responsible for switching in metal/molecule/metal systems are subjects of intense research. We report here a scanned probe technique that maps the conductance of a planar molecular junction (Pt/stearic acid monolayer/Ti) under mechanical perturbation by using an atomic force microscope (AFM) to apply a localized force to a molecular junction while measuring the junction conductance. Such mechano-conductance maps reveal that transport through the molecular device is dominated by nanoscale conducting channels, which emerged or disappeared when the junction is switched into higher or lower conductance states. A quantitative model that combines quantum tunneling with the growth of nano-asperities effectively describes the experimental conductance data across a wide range of device conductance.