Nanomaterials have been used extensively in the development of high sensitivity and high selectivity biodetection schemes.1–4 Designer particles, including noble‐metal polyhedral structures, quantum dots, nanopatterns, and nanorods have found application in many forms of biological tagging schemes, including DNA and protein detection, cell sorting, and histochemical staining.5–12 Significant advantages over conventional molecule‐based fluorophore strategies have been identified for several of these structures.13–15 Other applications for nanomaterials in biology, beyond diagnostics, include therapeutics and separations.9 A key area for researchers working with proteins involves separation and purification. Traditionally, nickel columns have been used in conjunction with histidine tagged proteins to separate such structures from a matrix of other undesirable biological elements. We and others have been working with nanorod structures prepared by the porous template synthesis approach pioneered by Martin and the group of Moskovits.16, 17 This synthetic procedure allows one to prepare rods electrochemically with uniform diameters and with predefined block lengths of inorganic and organic materials with excellent control.18, 19 We hypothesized that if nickel were introduced as one of the blocks in a single or multicomponent nanorod structure, it could be used as a magnetic nanosized affinity template for histidine tagged proteins and, therefore, an appropriately applied magnetic field could be used to effect separation of the protein–rod complex from a multicomponent solution. Herein, we demonstrate how one can use two‐component triblock ≈330 nm diameter rod structures with gold end blocks and a nickel interior block as materials that can very efficiently separate His‐tagged proteins from non‐his tagged structures. This work builds on our work with the transport of His‐tagged structures by dip‐pen nanolithography (DPN) to bulk solid‐state nickel oxide substrates and the work of others involving the generation of microscopic arrays of His‐tagged proteins on bulk nickel oxide substrates.20, 21