The use of magnetic microbeads in microfluidic systems is a promising approach for setting up lab on chips that accomplish a variety of bioanalytical operations. To meet the integration requirements of μTAS, one challenge is to reduce the size of magnetic effectors in order to increase the complexity of magneto-fluidic systems. In this paper, we report on a new method for manipulating batches of magnetic microbeads with exquisite spatial precision. Our approach is based on arrays of individually addressable micro-electromagnetic actuators, which are integrated in full polymer (SU-8) devices. We define the optimal working range of our technology, demonstrating that 5-turns micro-coils of ∼100μm in dimension efficiently trap 2.8μm microbeads in flow rates of ∼1μL/min. Furthermore we estimate quantitatively the magnetic forces generated by these micro-coils, which are on the order of 1–10pN. Taken together our technology affords reconfigurable and compact solutions for the manipulation of magnetic micro-particles in lab-on-chip applications.