In this paper, we report the development of two-dimensional scanning probe arrays to achieve high-throughput DPN writing in a parallel mode. A new "mold-and-transfer" micromachining process has been developed, which is capable of making large scanning probe arrays with high yield and at low cost. Up to date, two-dimensional passive probe arrays with 1000 metal probes and 1000,000 polymer probes have been successfully developed. Prototypes of two-dimensional active probe arrays have also been successfully fabricated and tested, which consists of 49 scanning probe individually controlled by a thermal bimorph micro actuator integrated on each probe. To ensure proper contact status of each probe on the sample surface, a new electrical probe-substrate contact sensing method has also been developed for two-dimensional DPN probe arrays to realize robust DPN writing. As such, 2D DPN writing has been successfully demonstrated for the first time.