A method is provided for forming a first via with an electrically conductive material, for example, copper, that is formed over and coupled to a conductive landing pad of an MRAM array. A sputter step is performed to lower the surface of the first via below that of a surrounding dielectric material. This recess is repeated in subsequent processing steps, providing alignment marks for the formation of a magnetic tunnel junction. The magnetic tunnel junction may be offset from the first via, and a second via being formed above the magnetic tunnel junction and to a conductive layer.