A scheme for magnetic based biomolecular separation, transportation and detection has been proposed, designed, fabricated and successfully demonstrated through a novel micro-fabricated magnetic system. Magnetic separation becomes a popular technique to purify or isolate cells, intracellular and biological active compounds from heterogeneous mixtures. This thesis introduces and demonstrates a fully micro-magnetic system as a magnetic potential concentrator for manipulating micro/nano magnetic particles in bio- molecular separation systems. The functional components of the device are an electrically phased planar electromagnet array and magnetic pillars positioned at specific locations above the surface of the planar electromagnets. The components are located in a microfluidic chamber with a capacity of 5 l. This system presents a new tool of magnetic control for manipulating and sampling biochemical compounds.