An extraordinary magnetoresistive sensor (EMR sensor) having a lead structure that is self aligned with a magnetic shunt structure. To form an EMR sensor according to an embodiment of the invention, a plurality of layers are deposited to form quantum well structure such as a two dimensional electron gas structure (2DEG). A first mask structure is deposited having two openings, and a material removal process is performed to remove portions of the sensor material from areas exposed by the openings. The distance between the two openings in the first mask defines a distance between a set of leads and the shunt structure. A non-magnetic metal is then deposited. A second mask structure is then formed to define shape of the leads.