deny *.php htaccess in uploads folder

Hi, in trying to secure my multisite network as much as possible and followed some advice and added an .htaccess file to my uploads folder containing:
<Files *.php>
Deny from all
</Files>

Post Indexer (and other plugins) load php files there.

I assume it will prevent the plugins from working, if so, is there something to add to the htaccess file to allow certain folders and/or .php files (folders better obviously)?

thanks