This paper describes a simple technique for fabricating complex, but well defined, three-dimensional (3D) networks of nanoscale flow paths in the channels of microfluidic systems. Near field scanning optical measurements reveal the optics associated with the fabrication process and the key features that enable its application to the area of microfluidics. Confocal studies of microfluidic devices that incorporate 3D nanostructures formed using this approach show that they function as efficient passive mixing elements, particularly at low Reynolds numbers. This application and others such as separation and extraction inmicrofluidic total analysis systems or lab on a chip devices represent promising areas for 3D nanostructures of this general type.