In our previous work we introduced the inverted MiniMag, a magnetic manipulation system capable of 5 degree-of-freedom (5-DOF) wireless control of micro- and nano structures. In this work, we implement a depth tracking algorithm to provide feedback on the z-position of manipulated particles in the absence of a side camera. We demonstrate 3D closed-loop servoing of magnetic microbeads along predefined trajectories. We successfully position magnetic microbeads functionalized with antibodies in close proximity to macrophages with sub-cellular resolution and record the phagocytosis of the beads. We also show that the system can be used for 3D targeted microtissue manipulation inside microfabricated devices.