Nanopillar arrays that are bactericidal but not cytotoxic against the host cells could be used in implantable medical devices to prevent implant-associated infections. It is, however, unclear what heights, widths, interspacing, and shape should be used for the nanopillars to achieve the desired antibacterial effects while not hampering the integration of the device in the body. Here, we present an in-silico approach based on finite element modeling of the interactions between Staphylococcus aureus and nanopatterns on the one hand and osteoblasts and nanopatterns on the other hand to find the best design parameters. We found that while the height of the nanopillars seems to have little impact on the bactericidal behavior, shorter widths and larger interspacings substantially increase the bactericidal effects. The same combination of parameters could, however, also cause cytotoxicity. Our results suggest that a specific combination of height (120 nm), width (50 nm), and interspacing (300 nm) offers the bactericidal effects without cytotoxicity.