A portable magnetic separator was proposed for in-vivo biomedical applications. In this prototype design, a matrix of alternating, parallel magnetizable wires, and biocompatible tubing is immersed into an externally applied magnetic field. The wires are magnetized and high magnetic fields as well as field gradients are created to trap blood-borne flowing magnetic nanospheres in the tube. In this paper, a parametric investigation was carried out to evaluate the capture efficiency of flowing magnetic nanospheres by a separator unit consisting of single tubing and four wires. The parameters include: mean blood velocity (1 to 20cm/s); magnetic field strength (0.1 to 2.0T); sphere size (500nm to 1000nm in radii); sphere magnetic material (iron, two types of magnetite) and magnetite content in the spheres (0.05 to 0.8 by weight); wire material (nickel, stainless steel 430, and Wairauite); wire length (2.0 to 20cm); wire size (0.125 to 1.0mm in radii); tubing size at a fixed ratio of tubing to wire diameter of unity. The results show that capture efficiencies of the spheres of well over 90% were achievable under reasonable human physiological conditions, provided that the mean blood velocities were below about 5.0cm/s. The results also show that the magnetic separator performance could be improved by maximizing the applied magnetic field strength up to about 1.0T and by reducing the size of the unit with tubing and wires of equal radii. The results help further optimize a prototype magnetic separator suitable for rapid sequestration of magnetic nanospheres from the human blood stream while accommodating necessary clinical boundary conditions.