Abstract: A method for manipulating a magnetic instrument within a lumen of a body, the method including the steps of: providing a system for manipulating the magnetic instrument, the system including an imaging instrument, a magnetic navigation system, a display device, an interface designed to steer the magnetic instrument, and a controller designed to control the system; providing the magnetic instrument; displaying an image of at least a magnetic distal portion of the magnetic instrument on the display device; sending via the interface an operator input to the system to change the direction of the magnetic field from a first direction to a second direction to steer the magnetic instrument in an advancement direction, wherein the operator input is made in reference to an imaging instrument coordinate system associated in a fixed manner to the imaging instrument; applying the magnetic field corresponding to the second direction.