While more than a decade of work has provided glimpses into the physics of highly charged ion (HCI) neutralization on surfaces, two prominent objectives remain unfulfilled: (1) a unified, quantitative model for separating the kinetic energy response of a wide range of materials classes from the effects of HCIs’ potential energy effects and (2) insertion of HCI technology(s) as a cost-effective processing tool in a high-volume market sector. The National Institute of Standards and Technology (NIST) electron beam ion trap (EBIT) facility has recently incorporated tools for preparing clean, atomically flat surfaces of single crystals from gold to tungsten to silicon and for depositing and patterning thin films that range from high resistivity oxides to transition metals like cobalt and nickel. Current activities are focused on utilizing this unique capability to simultaneously address both of the objectives above by employing technologically important magnetic multi-layer systems to perform transport measurements that provide new insight into the fundamental processes that occur during HCI–surface neutralization. Specifically, we are producing Magnetic Tunnel Junctions (MTJs) critical to both magnetic devices and incorporating HCIs in the processing recipe to adjust critical electronic properties that are currently inhibiting their advancement. In return, the electrical response of the tunnel junction to the HCI processing provides a novel approach to performing ensemble measurements of HCI–surface interactions. By varying the construction of the tunnel junction, critical tests of the role of electron density, densities of states and electronic structure in the HCI–surface charge exchange can be performed.