If you have some form of mod_rewrite going you can do this quite easily with a .htaccess file.
If you have something like this:
RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^(.*)$ index.php?url=$1 [QSA,L]
It will check that the file you are trying to access doesn't exist already. (Say you had a file hello.html that you still needed people to access via http://yoursite.com/hello.html)
Then if the file doesn't already exist it will load your index.php file with the rest of the URL stored in the url variable.
This means you can call something like this http://yoursite.com/pages/edit/24 and it will load index.php with /pages/edit/24 inside the url variable.
That should get you started and you won't need all kinds of folders and index pages, just mod_rewrite, .htaccess file and an index.php that will be used to load whatever you need.