External Programs

[eluser]bhbutter123[/eluser]
If I have most of my site run with codeigniter can I still use other programs with the site as well? For example, some of the programs I use I simply put into a subfolder of the site and then the url would look like http://somesite.com/external_program/index.php for the index page of the other application. With codeigniter rewriting the urls I am thinking I will not be able to do it, what do you think?