This study showcases two independent magnetic manipulation systems to remotely control the movement of Fe3O4 nanomaterial in microfluidic chips. One system utilizes a homogeneous rotating magnetic field to carry out magnetic stirring in 100 μm and 300 μm flow channels. The mixing results of this system revealed that adding Fe3O4 nanoparticles to the solution enhances the efficiency of the micromixer by twice as much that of a device without the nanomaterial. The second manipulation system utilizes oscillating magnetic field for rapid microablation of thrombus in a microchannel. A customizable magnetic platform using 3D-printed material is also constructed. This is proposed as a feasible low-cost and portable magnetic manipulation device that can implement both applications.