A method of navigating a medical device through a body of a patient includes providing a topography of at least a portion of the body, accepting user input defining a navigation path, robotically navigating the medical device to a starting point on the path, and robotically navigating the medical device along the navigation path to an endpoint. Waypoints defining the navigation path may be input on a graphical representation of the topography using a user interface such as a pointing device or touchscreen. The navigation path may also be defined by tracing a substantially continuous path on the graphical representation. A therapy may be administered while robotically navigating the medical device along the navigation path, either forward or in reverse, or while navigating the medical device along a return path defined by a plurality of virtual breadcrumbs generated as the medical device traverses the navigation path.