In this paper we present a lithographic process with the ability to automatically translate and arbitrarily position three-dimensional (3D) computer-generated patterns through the use of phase holograms. This method, dynamic maskless holographic lithography (DMHL), advances current photo-directed patterning and functionalization capabilities by expanding the capability to manipulate light in real-time without the use of expensive fixed masks. The system could be used for large-scale parallel manufacturing over larger areas and for point specific serial fabrication, interrogation, and metrology. The use of coherent illumination allows for the direct creation of 3D patterns of light for lithography as opposed to the mechanical stage, layer-by-layer 3D fabrication approach typical of direct-write systems. Extrinsic control over interfacial properties will provide a method for addressing aqueous phase bionanotechnolgy experimental systems in which detection, separation, transport, and handling are vital.