Linux uses a hierarchical file system structure with directories like /bin, /sbin, /etc to organize binaries, configuration files, and other resources. Users can navigate this structure using commands like cd, ls, and pwd. Files can be viewed, copied, moved, deleted and have their permissions and attributes modified using commands like cat, cp, mv, rm, chmod and chown. Output from commands can be redirected, piped to other commands, or used for command substitution. The find command allows searching for files.