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We have designed, fabricated and demonstrated a novel micro-system for programmable magnetic actuation using magnetic elliptical pathways on Si substrates. Lithographically patterned soft NiFe ellipses are arranged sequentially perpendicular to each other as stepping stones for the transport of magnetic beads. We have measured the magnetization curve of the ellipsoid (9 µm × 4 µm × 0.1 µm) elements with respect to the long and short axes of the ellipse. We found that the magnetization in the long axis direction is larger than that in the short axis direction for an applied field of ≤ 1,000 Oe, causing a force on carriers that causes them to move from one element to another. We have successfully demonstrated a micro-system for the magnetic actuation of biomolecule carriers of superparamagnetic beads (Dynabead ® 2.8 µm) by rotating the external magnetic field. This novel concept of magnetic actuation is useful for future integrated lab-on-a-chip systems for biomolecule manipulation, separation and analysis.