A magnetic head for use in a perpendicular recording system having a novel shield structure that provides exceptional magnetic shielding from extraneous magnetic fields such as from a write coil, shaping layer or return pole of the write head. The shield structure is constructed to have a bottom or leading surface that is generally coplanar with the bottom or leading surface of the shaping layer, but all or a portion of the shield structure is not as thick as the shaping layer so as to have a top surface that does not extend to the same elevation (in a trailing direction) as that of the shaping layer. Making the shields extend to a lower level than the shaping layer improves magnetic performance by reducing flux leakage from the write pole, and also provides manufacturing advantages, such as during the manufacturing of the write pole. These manufacturing advantages include the advantage of having the shields covered with a protective layer of, for example, alumina during the ion milling of the write pole.