We study the field-directed self-assembly and photothermal behavior of one-dimensional (1D) chains of core-shell Fe3O4@Au magnetic-plasmonic nanoparticles. Monte Carlo analysis is used to predict the self-assembly of the nanoparticles when they are subjected to a uniform magnetic field and confined to a fluidic nanochannel. A coupled photonic and thermodynamic analysis is performed to analyze the optical and photothermal properties of the 1D chain structures. We show for the first time that the assembled chain structures exhibit a pronounced dip in their absorption spectrum at a wavelength that is strongly sensitive to changes in the refractive index of the surrounding medium. The plasmon enhanced features of these structures are well suited for a variety of theranostic modalities as we discuss.