A three-degree of freedom, actuator-based system is described for positioning an ion current density probe within the near field region of plasma and ion thrusters. This system improves upon existing beam profiling systems which usually characterize plasma and ion beams by sweeping a Faraday probe through a single motion at a fixed axial (or radial) distance downstream of a device under test. Fully automated computer control is used for positioning the probe, data collection and analysis, and to interface via communication ports to power supply and vacuum chamber control systems. The three-axis probe actuator system is capable of obtaining improved ion beam data critical for calculating plume uniformity, beam symmetry, total energetic particle flux through a given plane, beam divergence, beam centroid, thrust vector direction, etc. The high resolution data collected with this tool are planned for use in validating numerical simulations of the plasma plume properties of ion and plasma thrusters. Experimental results are presented that demonstrate the capabilies of the beam profiling system on a Veeco Instruments 5-cm DC ion source. A total of 15 operating conditions were characterized by taking planar (x-y) scans of the ion beam at axial (z) distances ranging from 12.5 to 32.5 cm. Beam ion energies ranging from 200 to 1000 eV were evaluated at beam currents from 30 to 90 mA. The measurements were analyzed to calculate the effects of beam ion energy, beam current, and charge exchange and ion scattering on the beam shape and attenuation. The attenuation data were reduced to determine estimates of charge exchange cross section, and good agreement was observed with values available in the literature.