Sputtering systems and methods for packaging applications. In some embodiments, a method for processing a plurality of packaged devices can include forming or providing a first assembly having a stencil and a two-sided adhesive member attached to a first side of the stencil, with the stencil having a plurality of openings, and the two-sided adhesive member having a plurality of openings corresponding to the openings of the stencil. The method can further include attaching the first assembly to a ring to provide a second assembly, with the ring being dimensioned to facilitate a deposition process. The method can further include loading a plurality of packaged devices onto the second assembly such that each packaged device is held by the two-sided adhesive member of the first assembly and a portion of each packaged device extends into the corresponding opening of the two-sided adhesive member.