Dependence on ion beam energy, ion species, and incidence angles is investigated to reduce sidewall re-deposition on the magnetic tunnel junction barrier. Experimental and simulated etch data, for a representative spin-torque transfer random access memory structure with 40 nm critical dimension and 150 nm pitch, indicated a reduction in the sidewall re-deposition when operating at: high angle, high voltage, and with Xe as the source gas. The Monte Carlo binary collision model simulations showed re-deposition thickness reduced by ~75% with Xe versus Ar at 1 kV beam energy and 30° incidence angle.