Read this post http://dejanjanosevic.info/remove-index-php-permalink-in-wordpress/
This is not related to our theme. We are theme support, so we are able to help with issues related strictly to our theme, take it into account if you need help with default WordPress or WooCommerce questions. Contact WP or WC support if you have problems with default options.
Feel free to contact us anytime if you have questions related to our theme settings.