To remove index.php from url in your codeIgniter URL you have to create a .htaccess file in root directory where codeigniter is installed or where main index.php exists. If you put following code in .htaccess and save that file in your root you can use url system without index.php that way.
[php]
RewriteEngine on
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule .* index.php/$0 [PT,L]
[/php]