Abstract: The present invention provides a magnetic surgical instrument system for use in transmural surgical operations. The system includes at least two magnetic probes including magnetic components, such as a permanent magnet, an electromagnet, and a metal attracted to a magnet that attracts the magnetic probes to provide therewith a magnetic clamping force for clamping the wall of anatomical structures. The system may also include a driving device, which provides the driving signal to produce electromagnetic force and energy for various embodiments of the present invention, such as RF, microwave, laser, and cryogenic energy. The magnetic surgical system may also be adopted to ablate, cut, stable, and inject anatomical structure tissue clamped between the magnetic probes.