The scanning tunneling microscope (STM) is a unique tool for resolving the atomic-scale structure of surfaces and nanoclusters. In recent years, STM studies of model systems have made it possible to address many important, fundamental questions related to catalytic processes by imaging the atomic-scale structure of relevant systems, for example nanoclusters dispersed on surfaces. Here we highlight three prominent STM studies from our laboratories, all illustrating how the insight gained from STM studies of idealized model systems under vacuum conditions may be successfully linked to real high surface area catalyst systems operating under realistic conditions.