A portable separator has been developed to quantitatively separate blood-borne magnetic spheres in potentially high-flow regimes for the human detoxification purpose. In the separator design, an array of biocompatible capillary tubing and magnetizable wires is immersed in an external magnetic field that is generated by two permanent magnets. The wires are magnetized and the high magnetic field gradient from the magnetized wires helps to collect blood-borne magnetic nano/micro-spheres from the blood flow. In this study, a 3D numerical model was created and the effect of tubing-wire configurations on the capture efficiency of the system was analyzed using COMSOL Multiphysics 3.3 R . The results showed that the configuration characterized by bi-directionally alternating wires and tubes was the best design with respect to the four starting configurations. Preliminary in vitro experiments verified the numerical predictions. The results helped us to optimize a prototype portable magnetic separator that is suitable for rapid sequestration of magnetic nano/microspheres from the human blood stream while accommodating necessary clinical boundary conditions.