A stimulation system, such as a spinal cord stimulation (SCS) system, having a programmer with a user interface. The programmer determines a position of an implanted medical lead with respect to a patient's spinal column. The programmer overlays the medical lead, an initial stimulation field, and an initial target stimulation area within the initial stimulation field on an image of the spinal column. A user enters, via the user interface, graphical manipulations of displayed boundaries of the initial stimulation field and the initial target stimulation area. The graphical manipulations of the stimulation field and the target stimulation field are independent of each other and they may move and/or alter the shape of the boundaries. The programmer then determines stimulation parameters to drive the implanted medical lead to generate the displayed stimulation field and target stimulation field as manipulated by the user.