An array is formed with a protective cover on a substrate. The protective cover is patterned to produce an array of openings to the substrate. Desired material is deposited on the substrate through the openings. The protective cover may then be removed. In one embodiment, the protective cover is a conformal polymer, such as di-para-xylylene. It may be removed by mechanical peeling. The material may be biological material such as DNA. The protective cover may be used to prevent non-specific hybridization in inter-spot regions by performing hybridization with the cover still in place. Hybridization that occurs in such regions between the spots may be removed with removal of the protective cover.