I think this is a pretty simple question.
How do you an apache rewrite to hide a folder.
EX: www.website.com/pages/login.php to www.website.com/login.php
If your example actually reflects the files you need, then in your .htaccess file:
#Options +FollowSymLinks
RewriteEngine On
RewriteRule ^/pages/(.+)\.php $1\.php [NC, L]
Also, if the directory has read permission, it cannot be, in reality "hidden". I assume you mean that it no longer appears in the url.