Bacteria　killing　behavior　based　on　physical　effects　is　preferred　for　biomedical　implants　because　of　the　negligible　associated　side　effects.　However,　our　current　understanding　of　the　antibacterial　activity　of　nanostructures　remains　limited　and,　in　practice,　nanoarchitectures　that　are　created　on　orthopedics　should　also　promote　osteogenesis　simultaneously.　In　this　study,　tilted　and　vertical　nanolamellar　structures　are　fabricated　on　semi-crystalline　polyether-ether-ketone　(PEEK)　via　argon　plasma　treatment　with　or　without　pre-annealing.　The　two　types　of　nanolamellae　can　physically　kill　the　bacteria　that　come　into　contact　with　them,　but　the　antibacterial　mechanisms　between　the　two　are　different.　Specifically,　the　sharp　edges　of　the　vertically　aligned　nanolamellae　can　penetrate　and　damage　the　bacterial　membrane,　whereas　bacteria　are　stuck　on　the　tilted　nanostructures　and　are　stretched,　leading　to　eventual　destruction.　The　tilted　nanolamellae　are　more　desirable　than　the　vertically　aligned　ones　from　the　perspective　of　peri-implant　bone　regeneration.　Our　study　not　only　reveals　the　role　of　the　arrangement　of　nanostructures　in　orthopedic　applications　but　also　provides　new　information　about　different　mechanisms　of　physical　antibacterial　activity.　©　2023　The　Royal　Society　of　Chemistry.