The invention provides multisegmented, multifunctional magnetic nanowires for the probing and manipulation of molecules at the cellular and subcellular level. The different segments of the nanowire may have differing properties, including a variety of magnetic, non-magnetic, and luminescent behavior. Differences in surface chemistry allow different segments of a single nanowire to be functionalized with different multiple functional groups and/or ligands, giving the wire chemical multifunctionality.