Restricting access to top level folder

[eluser]frist44[/eluser]
I have a folder that I'm allowing content to be uploaded to. The folder is at the same level as the root 'index.php'. What's the best way to restrict access to this folder and all subfolders. There will presumably be many subfolders, so I would rather something simple from the top level. I would also like to have internal CI scripts be able to access the folder, just not from a direct URL call.

Thanks!

[eluser]bretticus[/eluser]
[quote author="frist44" date="1265103244"]I have a folder that I'm allowing content to be uploaded to. The folder is at the same level as the root 'index.php'. What's the best way to restrict access to this folder and all subfolders.[/quote]

htaccess Allow Deny