A system and method of managing files and a memory device are provided. The system for managing files includes an attribute-management module designating nested attributes to the files having a size smaller than a basic allocation unit of a file system or to directories to which the files belong, a data-management module adjacently nesting the files to which the nested attributes are designated by the attribute-management module with no empty space between the files, and a metadata-management module writing start offsets of the files nested by the data-management module in metadata of the files.