Atomically thin, two-dimensional transition metal dichalcogenides (TMDCs) have attracted great interest as a new direct band gap semiconducting materials. Scalable nanoscale manufacturing and controllable modulation of optoelectronic properties of TMDCs are of fundamental importance to enable a wide range of future nanodevices. In this work, programmable DNA nanostructures are self-assembled into desired shape and dimension, and they serve as lithographic templates for patterning TMDCs. The nanostructured TMDCs are analyzed and verified by atomic force microscopy and Raman spectroscopy. In addition, a modulation of the optoelectronic properties of TMDCs are demonstrated by interfacing them with phthalocyanine molecules. The photoluminescence emission can be selectively and reversibly engineered through electron transfer from photoexcited TMDCs to functionalized molecules. The results demonstrated here could be further applicable to other 2D materials for future nanoscale electronics, sensors, and optoelectronic devices.