A method for forming a via in an alumina protective layer on a structure such as a magnetic write head for use in perpendicular magnetic recording. A substrate such as an alumina fill layer, magnetic shaping layer, etc. is formed with region having a contact pad formed therein. A structure such as a magnetic pole, and or magnetic trailing shield, is formed over the substrate and is covered with a thick layer of alumina. The alumina can be applied by a high deposition rate process that does not form voids or seams in the alumina layer. The alumina layer can then be planarized by a chemical mechanical polishing process (CMP) and then a mask structure, such as a photoresist mask, is formed over the alumina layer. The mask structure is formed with an opening disposed over the contact pad. A reactive ion mill is then performed to remove portions of the alumina layer that are exposed at the opening in the mask, thereby forming a via in the alumina layer. The mask can then be lifted off and an electrically conductive material can be deposited into the via. Forming the via by a subtractive method rather than by a liftoff process allows the alumina to be deposited in a manner that does not result in voids. The use of reactive ion milling allows the via to be well defined and formed with substantially vertical side walls rather than in a conical or outward spreading fashion as would be formed by other material removal processes such as wet etching.