A metal film is formed over a resin layer including a plurality of multi-depth depressions (MDP) separated by interstitial regions, each MDP including a deep portion and an adjacent shallow portion. A sacrificial layer is formed over the metal film. The sacrificial layer and metal film are sequentially dry etched to expose a resin layer surface at the shallow portion and interstitial regions. Resin layer portions are removed i) at the shallow portion to form a depression region having a surface directly adjacent to a surface at the deep portion and ii) at the interstitial regions to form new interstitial regions surrounding the deep portion and the depression region. First functionalized layer is deposited over the metal film, depression region, and new interstitial regions. The metal film is removed from the deep portion. Second functionalized layer is deposited over the surface at the deep portion. New interstitial regions are polished.