A magnetic manipulation system and method for moving and navigating a magnetic device in a body are provided. The system includes a robotic parallel mechanism having at least three electromagnets and at least three electromagnetic coils coupled to the at least three electromagnets, respectively. The electromagnetic coils are actuated to keep the electromagnets in static conditions or move the electromagnets along a desired trajectory, a current control unit supplying currents to the electromagnetic coils which have soft iron cores. The currents supplied by the control unit are configured to generate dynamic magnetic field in the soft iron core's linear region. The current control unit and the robotic parallel mechanism are configured to generate desired dynamic magnetic fields in desired positions within a workspace to control a magnetic device, and a three-dimensional position sensor is configured for performing a close loop control of the robotic parallel mechanism.