Magnetic actuation of microscopic beads is a promising technique for enhancement and manipulation of scalar transport in micro-fluidic systems, in particular, for biosensors. Fundamental to micro-fluidic transport, notwithstanding the diversity in systems, is that it happens under laminar flow conditions. Moreover, given that bead actuation typically involves sequences of rotations and translations in multiple directions, thus implying three-dimensional (3D) unsteady flow conditions, transport in the current class of systems is essentially 3D and unsteady. The present study addresses fundamental transport phenomena in such configurations in terms of 3D coherent structures formed by the Lagrangian fluid trajectories in a 3D time-periodic flow driven by an actuating sphere. Such structures geometrically determine the transport properties and insight into their formation, characteristics and response to parametric variations is key to better understanding and, ultimately, systematic manipulation of 3D transport. The study thus offers important new insights into a class of flow configurations with great practical potential.