A magnetic field guided crystal orientation system, and a method of operation of a magnetic field guided crystal orientation system thereof, including: a work platform; a heating element above the work platform for selectively heating a base layer having grains on a wafer substrate where the wafer substrate is a part of a wafer on the work platform; and a magnetic assembly fixed relative to the heating element for aligning the grains of the base layer using a magnetic field of 10 Tesla or greater for formation of an interconnect having a crystal orientation of grains in the interconnect matching the crystal orientation of the grains of the base layer.