The transport of free ions through highly under-expanded jet flows of neutral gases and in the presence of applied electric fields is investigated by continuum-based (fluid) numerical simulations. In particular, numerical results are described which are relevant to ion flows occurring in quadrupole interfaces of mass spectrometer systems. A five-moment mathematical model and parallel multi-block numerical solution procedure are developed for predicting the ion transport. The model incorporates the effects of ion-neutral collision processes and is used in conjunction with a Navier-Stokes model and flow solver for the neutral gas to examine the key influences controlling the ion motion. The effects of the neutral gas flow, electric fields (both dc and rf) and flow field geometry on ion mobility are carefully assessed. The capability of controlling the charged particle motions through a combination of directed neutral flow and applied electric field is demonstrated for these high-speed, hypersonic, jet flows. The neutral dynamics is shown to have a strong influence on the ion transport whereas the electric field imparts a more gradual effect. The combined effect of the applied (dc and rf) electric field and neutral collision processes with the dilute neutral gas results in a strong tendency for ion focusing towards the axis of symmetry, with the overall efficiency governed by the mass-to-charge ratio.