A program I use, to create search engine friendly URL's requires this in my .htaccess

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*) index.php

Will the search engines mind this?

The problem I have when I use this that I can not get to my cgi-bin directory and I do not know why.

Any thoughts?