In thin-film systems, effects induced by interfaces play a crucial role which makes them the source of many important magnetic properties (e.g., the perpendicular magnetic anisotropy, interfacial Dzyaloshinskii-Moriya interaction, etc.). Therefore, the ability to design interfaces in controlled ways is very important. Here, we will show that a proper choice of Ga+ ion energy permits control of modification efficiency at the bottom and at the top interfaces. We used this fact to tune the perpendicular magnetic anisotropy of an Ir/Co/Pt layered system. Analyzing the experimental data and Monte-Carlo simulations using TRIDYN code, we found that the mixing of elements is stronger for the top interface (Co/Pt) than for the bottom interface (Ir/Co) and this difference can be enhanced by reducing the ion energy. This technique opens a new way to control the magnetic properties of layered systems on which structural asymmetries (between the bottom and top interfaces of the magnetic layer) influence magnetic properties.