Electroreduction of diazonium salts is a widely used technique for grafting organic films on various surfaces. In this paper, scanning electrochemical microscopy (SECM) was used for high resolution characterization of a thiolated aryl multilayer film obtained by electrografting of thiophenol diazonium on highly ordered pyrolytic graphite (HOPG). The blocking properties of the film were evaluated, and the origins of incomplete surface passivation were elucidated by comparing current distance curves and surface reactivity maps obtained with nanometer- and micrometer-sized tips. In this way, one can distinguish between different pathways of charge transport in the film, e.g., pinhole defects versus rate-limiting charge transfer through the film. Pd nanocubes were anchored to the film by thiol groups and imaged by SECM. The applicability of SECM to in situ visualization of the geometry of non-spherical nanoparticles has been demonstrated.