"System files" usually means files with both the S (system) and H (hidden) attribute set. There is an option to hide them in Preferences, although if Hidden files are already hidden then that takes care of both.
If you're seeing (unusual) files with only the S attribute and not the H attribute, neither option will hide those, but you can hide them via Folder Options, on the tabs for hiding things, then save the format for all folders as per Folder Formats: Quick Guide