Conjugated magnetic nanoparticles have recently demonstrated potential in activating unique and specific activity within cells. Leveraging microfabrication, we have developed a technique of localizing nanoparticles to specific, subcellular locations by a micropatterned ferromagnetic substrate. Controlled patterns of nanoparticles were assembled and dynamically controlled with submicrometer precision within live cells. We anticipate that the technique will be useful as a compact, simple method of generating localizable, subcellular chemical and mechanical signals, compatible with standard microscopy.