As an important development of medical instrumentation, minimally invasive therapeutic operations have been recently introduced. The foremost element of minimally invasive techniques is navigating a micro-device through human body, especially inside blood vessels. A remote actuation over the micro-device is normally provided by electromagnetic actuators. In most applications, a control scheme is also required to initiate the actuation force, the magnetic propulsion, such that at every time step, the micro-device moves towards or along a given path. This paper contributes in development of the electromagnetic system model mostly used in magnetic navigation systems to be representable in control affine form. Next, a multi-input multi-output (MIMO) trajectory tracking controller is designed to conduct the auto-navigation of the device along a given path. This method is a generalised version of a semi-global nonlinear output regulation' introduced for single-input single-output (SISO) systems. Finally, the proposed scheme is examined for an iron particle moving in a fluidic environment. The simulation results show fast decay in deviation of the particle position from the reference path under some assumptions. This shows that the proposed scheme can be offered for medical applications.