We numerically examine the manipulation of superconducting vortices interacting with a moving trap representing a magnetic force tip translating across a superconducting sample containing a periodic array of pinning sites. As a function of the tip velocity and coupling strength, we find five distinct dynamic phases, including a decoupled regime where the vortices are dragged a short distance within a pinning site, an intermediate coupling regime where vortices in neighboring pinning sites exchange places, an intermediate trapping regime where individual vortices are dragged longer distances and exchange modes of vortices occur in the surrounding pins, an intermittent multiple trapping regime where the trap switches between capturing one or two vortices, and a strong coupling regime in which the trap permanently captures and drags two vortices. In some regimes we observe the counterintuitive behavior that slow moving traps couple less strongly to vortices than faster moving traps; however, the fastest moving traps are generally decoupled. The different phases can be characterized by the distances the vortices are displaced and the force fluctuations exerted on the trap. We find different types of stick-slip motion depending on whether vortices are moving into and out of pinning sites, undergoing exchange, or performing correlated motion induced by vortices outside of the trap. Our results are general to the manipulation of other types of particle-based systems interacting with periodic trap arrays, such as colloidal particles or certain types of frictional systems.