Background Due to the increased emergence of antimicrobial resistance, alternatives to minimize the usage of antibiotics become attractive solutions. Biophysical manipulation of material surface topography to prevent bacterial adhesion is one promising approach. To this end, it is essential to understand the relationship between surface topographical features and bactericidal properties in order to develop antibacterial surfaces. Results In this work a systematic study of topographical effects on bactericidal activity of nanostructured surfaces is presented. Nanostructured Ormostamp polymer surfaces are fabricated by nano-replication technology using nanoporous templates resulting in 80-nm diameter nanopillars. Six Ormostamp surfaces with nanopillar arrays of various nanopillar densities and heights are obtained by modifying the nanoporous template. The surface roughness ranges from 3.1 to 39.1 nm for the different pillar area parameters. A Gram-positive bacterium, Staphylococcus aureus, is used as the model bacterial strain. An average pillar density at ~ 40 pillars μm−2 with surface roughness of 39.1 nm possesses the highest bactericidal efficiency being close to 100% compared with 20% of the flat control samples. High density structures at ~ 70 pillars μm−2 and low density structures at < 20 pillars μm−2 with surface roughness smaller than 20 nm reduce the bactericidal efficiency to almost the level of the control samples. Conclusion The results obtained here suggests that the topographical effects including pillar density and pillar height inhomogeneity may have significant impacts on adhering pattern and stretching degree of bacterial cell membrane. A biophysical model is prepared to interpret the morphological changes of bacteria on these nanostructures.