Purple membranes from the archaeon Halobacterium salinarum consist of !D crystals of the light-driven proton pump bacteriorhodopsin, which convert photons into a proton gradient across the cell membrane. This functional feature and the structural rigidity make them appealing candidates for integration into biomimetic devices. To this end, and in order to carry out their function, purple membranes must be positioned in the correct orientation at the position of interest. Precise placement and control over the orientation of nanoscale objects still constitutes a formidable challenge. Here, it is shown that isolated purple membrane patches can be transported and positioned at predefined locations in nanofluidic confinement, with control over their orientation at the target sites. The transport is achieved through a rocking Brownian motor scheme, while the controlled deposition of the membranes is realized by engineering the surface potential of a fluid-filled nanofluidic slit. This controlled manipulation of purple membrane patches outlines a new pathway toward the integration of biological or other delicate supramolecular structures into top–down-fabricated patterns, for the assembly of nanoscale hybrid devices that serve as a light-driven source of (chemical) energy.