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In some magnetic beads based lab-on-chip (LoC) applications, such as purification and fast cell detection, high throughput capacity is required. In this paper, we propose an optimization method for the implementation of in-channel planar microcoils array. By generating more dispersed trapping centers and exploiting the array scanning scheme, the problem of interaction among magnetic beads is controlled and both power consumption and Joule heating are reduced. Simulation results by Finite Element Analysis software show that under the first order optimization, the proposed topology saves 69% power, while keeps approximate total trapping area, compared with the conventional topologies. The microfluidic structure combining the proposed coils array and operation scheme is suitable for high throughput LoC applications.