A reticle comprising isolated pillars is configured for use in imprint lithography. In some embodiments, on a first substrate a pattern of pillars pitch-multiplied in two dimensions is formed in an imprint reticle. The imprint reticle is brought in contact with a transfer layer overlying a series of mask layers, which in turn overlie a second substrate. The pattern in the reticle is transferred to the transfer layer, forming an imprinted pattern. The imprinted pattern is transferred to the second substrate to form densely-spaced holes in the substrate. In other embodiments, a reticle is patterned by e-beam lithography and spacer formations. The resultant pattern of closely-spaced pillars is used to form containers in an active integrated circuit substrate.