Achieving ultrasmall dimensions of materials and retaining high throughput are critical fabrication considerations for nanotechnology use. This article demonstrates an integrated approach for developing isolated sub-20 nm silicon oxide features through combined "top-down" and "bottom-up" methods: nanoimprint lithography (NIL) and block copolymer (BCP) lithography. Although techniques like those demonstrated here have been developed for nanolithographic application in the microelectronics processing industry, similar approaches could be utilized for sensor, fluidic, and optical-based devices. Thus, this article centers on looking at the possibility of generating isolated silica structures on substrates. NIL was used to create intriguing three-dimensional (3-D) polyhedral oligomeric silsesquioxane (POSS) topographical arrays that guided and confined polystyrene-block-poly(dimethylsiloxane) (PS-b-PDMS) BCP nanofeatures in isolated regions. A cylinder forming PS-b-PDMS BCP system was successfully etched using a one-step etching process to create line-space arrays with a period of 35 nm in confined POSS arrays. We highlight large-area (>6 μm) coverage of line-space arrays in 3-D topographies that could potentially be utilized, for example, in nanofluidic systems. Aligned features for directed self-assembly application are also demonstrated. The high-density, confined silicon oxide nanofeatures in soft lithographic templates over macroscopic areas illustrate the advantages of integrating distinct lithographic methods for attaining discrete features in the deep nanoscale regime.