Efficient T cell isolation with high recovery and high purity is important for academic and clinical research. Using our newly developed MARS system (multi-physics automated reconfigurable separation) we demonstrate an automated process to isolate T cells within a short time. With MARS Bar, we achieved greater than 95% purity of T cells isolated from a blood sample with a recovery higher than 90%. Furthermore, separated T cells were shown to have preserved activation and proliferation, necessary for further functional studies.