We have developed an efficient, one-step method to create magnetic nanowires consisting of permanently-linked chains of magnetic beads of varying flexibility tethered to a patterned glass surface using simple amidation chemistry. The magnetic beads have core-shell structure and were prepared by layer by layer assembly. The flexibility of the nanowire was governed by the molecular weight of the molecule used to covalently link the beads, and its length by the height of the microchannel in which it was synthesized. The nanowire diameter was determined both by the bead size, and by the number of beads adhering to each dot in the microstamped, patterned array. Longer nanowires can form loops attached at two points on the glass surface. Both single flexible chains and flexible loops can adopt different configurations (straight, hairpin, S-shaped, etc.) when subjected to magnetic fields, the configurations depending on the directions of these fields. Shorter, less flexible nanowires align with the field always and do not exhibit the more exotic configurations seen for long, flexible chains and loops. These magnetic nanowires can have potential use in microfluidic pumping and mixing processes and in microparticle manipulation.