Co/Pt thin film multilayers with strong perpendicular anisotropy and out-of-plane coercivities of 5-11 kOe were magnetically altered in areas of local ion beam interaction. The ion irradiations were performed by ion projection through silicon stencil masks fabricated by silicon on insulator (SOI) membrane technology. The ion projector at the Fraunhofer Institute for Silicon Technology (ISiT) was operated at 73 keV ion energy and with a 8.7- fold demagnification. After exposure to 3 × 1014Ar+/ cm2 magnetic islands smaller than 100 nm in diameter were resolved in the Co/Pt multilayersby means of magnetic force microscopy. The impact of different ion species (He+, Ar+ and Xe+) and ion energies (10 – 200 keV) on the multilayer structure was evaluated using Monte Carlo simulations. The ballistic interface intermixing was used to predict magnetic coercivity changes for various irradiation conditions. The simulations revealed that with 73 keV Ar+ and Xe+ ions the irradiation dose could be reduced by a factor of 100 and 400 respectively in comparison to 73 keV He+which was verified in the experiments. X-ray reflectivity measurements confirmed that the Co/Pt superlattice structure is slightly weakened during the irradiation and that the surface smoothness of the media is preserved. Using the Ion Projection Process Development Tool (PDT) at IMS-Vienna concentric data tracks including head positioning servo informations were patterned onto a 1” IBM microdrive™ glass disk which was coated with Co/Pt multilayers. In a single exposure step several tracks within an exposure field of 17 mm in diameter were structured by 2 × 1015He+/ cm2 at 45 keV using a 4- fold demagnification set-up.