Provided are methods and systems for forming discreet multilayered structures. Each structure may be deposited by in situ deposition of multiple layers at one of multiple site isolation regions provided on the same substrate for use in combinatorial processing. Alignment of different layers within each structure is provided by using two or more differently sized openings in-between one or more sputtering targets and substrate. Specifically, deposition of a first layer is performed through the first opening that defines a first deposition area. A shutter having a second smaller opening is then positioned in-between the one or more targets and substrate. Sputtering of a second layer is then performed through this second opening that defines a second deposition area. This second deposition area may be located within the first deposition area based on sizing and alignment of the openings as well as alignment of the substrate.