The best way to do this, is by using a single index.php as the entry point for every request. Let that index.php do the routing (including and executing other PHP files) base on the request uri ($_SERVER["REQUEST_URI"]). You can use the following UrlToolkit to do the rewriting:
UrlToolkit {
ToolkitID = my_toolkit
RequestURI exists Return
Match .* Rewrite /index.php
}
Protect the other PHP files from being requested directly, by placing them outside the website root or by checking for a constant which was set in index.php. You could also prevent it via an UrlToolkit rule, to be placed before the last rule:
Match \.php DenyAccess