First of all make sure to remove index.php from $config['index_page'] = ''; in your config.php then turn on readwrite_mode and add this to your htaccess file
RewriteEngine on
RewriteBase /
# Hide the application and system directories by redirecting the request to index.php
RewriteRule ^(application|system|\.svn) index.php/$1 [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php/$1 [QSA,L]