WordPress File Manager is a great plugin for managing sub-folders and other files in the back-end.
However, the default directory is set to the site root. If you dont want your users to have access to your WP installation files, it’s best to change this to a different folder.

To change this setting edit the plugin files (shortcut here)

'path'	=> ABSPATH.'/wp-content/uploads/',	// path to files (REQUIRED)
'URL'	=> site_url().'/wp-content/uploads/',	// URL to files  (REQUIRED)

Like this: