A Monte Carlo simulation of the metal flux from a small scale rotating cylindrical magnetron is presented. The model describes the sputtered particles trajectories through the gas in a user definable 3D set-up. The ejection positions of the sputtered particles are generated according to the simulated ion current density on the target. The thermal motion of the background gas is included, with collisions modelled based on either quantum chemical or screened Coulomb interaction potentials. Experimental characterization of the metal flux was performed for Cu, Al and Ti targets at a range of argon pressures (0.3–1 Pa) by measuring deposition rate distributions. A comparison with preliminary simulations showed the importance of a correct description of the nascent angular distribution of the sputtered particles. Therefore, this distribution was not considered as given by sputter simulation or analytical formula, but was instead reconstructed from the low pressure experimental deposition profiles. The typical heart-like shaped emission observed at low energy sputtering was found and a comparison was made with results from binary collision approximation modelling. The spatial, pressure and material dependence of the metal flux in the chamber was then simulated and found to be in good agreement with the experiment.