The results of numerical simulation of plasma‐based, porous, template‐assisted nanofabrication of Au nanodot arrays on highly‐doped silicon taking into account typical electron density of low‐temperature plasma of 1017–1018 m−3 and electron temperature of 2–5 eV are reported here. Three‐dimensional microscopic topography of ion flux distribution over the outer and inner surfaces of the nanoporous template is obtained via numerical simulation of Au ion trajectories in the plasma sheath, in the close proximity of, and inside the nanopores. It is shown that, by manipulating the electron temperature, the cross‐sheath potential drop, and by additionally altering the structure of the nanoporous template, one can control the ion fluxes within the nanopores, and eventually maximize the ion deposition onto the top surface of the developing crystalline Au nanodots (see top panel in the figure). In the same time, this procedure allows one to minimize amorphous deposits on the sidewalls that clutter and may eventually close the nanopores, thus disrupting the nanodot growth process, as it is shown in the bottom panel in the figure on the right.