Ferromagnetic micro-columns (FMCs) have been fabricated on glass substrates using standard photolithography and electroplating and then integrated in micro-fluidic channels in order to study the response of super-paramagnetic beads suspended in an aqueous solution. We observed that under low external magnetic fields, the integrated micro-columns could generate sufficiently strong magnetic field gradients to trap super-paramagnetic beads in a flowing stream of water. The trapping behavior of the integrated FMCs was studied by considering different micro-patterns and different magnetic field intensities. In addition, the formation of magnetic micro-beads chains has been observed due to the magnetic dipole interactions. We believe that the integration of ferromagnetic micro-columns in microfluidic channels can have a variety of advanced applications, considering different possibilities of surface functionalization and manipulation of super-paramagnetic beads in an aqueous solution.