A system for superimposing virtual anatomical landmarks on an image includes a medical positioning system (MPS) for producing location readings with respect to points within a region of interest in accordance with an output of a location sensor disposed in a medical device. A coordinate system of the MPS is registered with an image coordinate system. A control unit receives a signal from a user to record a location reading when the medical device is at a desired point in the region of interest where the user desires to place a virtual landmark, modifies the recorded location reading for motion compensation, transforms the motion-compensated location reading from the MPS coordinate system to the image coordinate system to produce a target location, and then superimposes a representation of the virtual landmark on the image at the target location.