A three dimensional electrode structure for flow-through micro electroporation is proposed to achieve well-controlled cell positioning in a confined region. In this structure, cell position is actively performed by using dielectrophoresis in a three dimensional electrode structure. Compared with conventional planar electrode structures, the proposed electrode structure can achieve excellent aligning of cells not only in horizontal dimension but also in vertical dimension for receiving uniform electrical field during electroporation. The effectiveness of the proposed structure is validated by both numerical simulation using a commercial tool, CFD-ACE+, and experiments using the fabricated microfluidic chip. The results are compared with conventional parallel finger electrode structures under the same conditions.