Precision nanoscale deposition is a fundamental requirement for much of current nanoscience research. Further, depositing a wide range of materials as nanoscale features onto diverse surfaces is a challenging requirement for nanoscale processing systems. As a high resolution scanning probe-based direct-write technology, Dip Pen Nanolithography® (DPN®) satisfies and exceeds these fundamental requirements. Herein we specifically describe the massive scalability of DPN with two dimensional probe arrays (the 2D nano PrintArray™). In collaboration with researchers at Northwestern University, we have demonstrated massively parallel nanoscale deposition with this 2D array of 55,000 pens on a centimeter square probe chip. (To date, this is the highest cantilever density ever reported.) This enables direct-writing flexible patterns with a variety of molecules, simultaneously generating 55,000 duplicates at the resolution of single-pen DPN. To date, there is no other way to accomplish this kind of patterning at this unprecedented resolution. These advances in high-throughput, flexible nanopatterning point to several compelling applications. The 2D nano PrintArray can cover a square centimeter with nanoscale features and pattern 107 μm2 per hour. These features can be solid state nanostructures, metals, or using established templating techniques, these advances enable screening for biological interactions at the level of a few molecules, or even single molecules; this in turn can enable engineering the cell-substrate interface at sub-cellular resolution.