One of the most challenging but potentially rewarding goals in nanoscience is the ability to direct the assembly of nanoscale materials into functional architectures with high yields, minimal steps, and inexpensive procedures. Despite their unique physical properties, the inherent difficulties of engineering wafer-level arrays of useful devices from nanoscale materials in a cost-effective manner have provided serious roadblocks toward technological impact. To address nanoscale features while still maintaining low fabrication costs, we demonstrate here an inexpensive printing method that enables repeated patterning of large-area arrays of nanoscale materials. DNA strands were patterned over 4 mm areas with 50 nm resolution by a soft-lithographic subtraction printing process, and DNA hybridization was used to direct the assembly of sub-20 nm materials to create highly ordered two-dimensional nanoparticle arrays. The entire printing and assembly process was accomplished in as few as three fabrication steps and required only a single lithographically templated silicon master that could be used repeatedly. The low-cost procedures developed to generate nanoscale DNA patterns can be easily extended toward roll-to-roll assembly of nanoscale materials with sub-50 nm resolution and fidelity.