This paper provides a unique strategy for controlling integrated hollow nanostructure arrays such as boxes or pillars at the nanometer scale. The key merit of this technique is that it can overcome resolution limits by sidewall deposition and deposit various materials using a sputtering method. The sputtering method can be replaced by other dry deposition techniques such as pulsed laser deposition (PLD) for complex functional materials. Furthermore, it can produce low-cost large-area fabrication and high reproducibility using the NIL (nanoimprint lithograph) process. The fabrication method consists of a sequence of bilayer spin-coating, UV-NIL, RIE (reactive ion etching), sputtering, ion milling and piranha cleaning processes. By changing the deposition time and molds, various thicknesses and shapes can be fabricated, respectively. Furthermore, the fabricated Au box nanostructure has a bending zone of the top layer and a approximately 17 nm undercut of the bottom layer as observed by SEM (scanning electron microscope). The sidewall thickness was changed from 12 to 61 nm by controlling the deposition time, and was investigated to understand the relationship with blanket thicknesses and geometric effects. The calculated sidewall thickness matched well with experimental results. Using smaller hole-patterned molds, integrated nanobox arrays, with inner squares measuring approximately 160 nm, and nanopillar arrays, with inside pores measuring approximately 65 nm, were fabricated under the same conditions.