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A micro-pillar array (MPA) is proposed in this paper to trap and separate magnetic beads (MBs) in microfluidic systems. MBs are used in many biomedical applications due to being compatible in dimension to biomolecules, the large surface area available to attach biomolecules, and the fact that they can be controlled by a magnetic field. Trapping and separating these labeled biomolecules is an important step toward achieving reliable and accurate quantification for disease diagnostics. Nickel Iron (Ni50Fe50) micro-pillars were fabricated on a Silicon (Si) substrate by standard microfabrication techniques. Experimental results showed that MBs could be trapped on the MPA at the single bead level and separated from other non-target particles. This principle can easily be extended to trap and separate target biomolecules in heterogeneous biological samples.