First, your webserver should only recognise *.php as php scripts, and leave the rest alone.
There are a few things you can do.
a) move the uploaded files to a directory outside the documentroot. That way any malicious files can nolonger be accessed directly and are therefore safe.
If you want make the files downloadable, you can make a PHP script that will load the file into memory and pass it on to the client without executing it.
b) Recognise PHP scripts.
Check for .php files and rename them to .phps, which will make the webserver print and the script with syntax-highlighting instead of executing it.
c) Invalidate PHP scripts.
Look for the <?php tag and replace it with <pre>. that way PHP can't find a 'start of php-block' marker and it will not execute the code.