The deposition of a thin film on a substrate surface can be achieved with a wide variety of techniques. Deposition using low energy ion beams is not a common technique, but it yields promising features, due to the hyperthermal nature of the deposited ions. With low energy ion deposition, it is possible to grow films with good characteristics at significantly lower temperatures compared to thermal deposition. The quality of these films critically depends on the energy of the impinging ions. We investigated the influence of the energy on the surface morphology for the deposition of Co onto Si(111). The roughness of this surface decreases significantly when the ion energy is increased, until it reaches a minimum at 25 eV. When the ion energy is further increased, the surface roughness increases again. This behavior can be explained by taking into account the interplay between the beneficial and detrimental effects due to the ion energy. Beneficial effects such as enhanced mobility and improved layer-by-layer growth cause a decrease in surface roughness when the deposition energy is increased from thermal to 25 eV. For energies above that value, undesirable effects such as defect creation and pileup dominate, leading to an increase in surface roughness. This study shows that low energy ion deposition can be used to improve the surface quality of a thin film by choosing the optimal deposition energy.