How can I block a folder from WP custom permalinks?

I have a WP blog installed in the root folder and I installed a separate PHP program in a new sub folder. When I go to activate the PHP program in the subfolder it comes up with a 404 error page not found because my WP custom permalinks are changing the filenames in my subfolder where the PHP program is located.

So is there some code that I can put in my WP root folder htaccess file that will prevent the custom permalinks from affecting my subfolder where I have the separate PHP program?

Thanks!
LFNNS