Remove USPS Priority Flat Rate envelopes, add to your theme functions.php file

gistfile1.php

/**
 * Remove USPS Flat rate envelopes from the available options
 * Once added the customer will not see any rates for envelopes
 */
add_filter( 'usps_flat_rate_boxes', 'custom_usps_flat_rate_boxes' );
function custom_usps_flat_rate_boxes( $flat_rate_boxes ) {

	unset($flat_rate_boxes["d29"]);
	unset($flat_rate_boxes["d30"]);
	unset($flat_rate_boxes["d63"]);
	unset($flat_rate_boxes["d16"]);
	unset($flat_rate_boxes["d38"]);
	unset($flat_rate_boxes["d40"]);
	unset($flat_rate_boxes["d42"]);
	unset($flat_rate_boxes["d44"]);
	unset($flat_rate_boxes["d13"]);

	unset($flat_rate_boxes["i33"]);
	unset($flat_rate_boxes["i30"]);
	unset($flat_rate_boxes["i63"]);
	unset($flat_rate_boxes["i8"]);
	unset($flat_rate_boxes["i29"]);

	return $flat_rate_boxes;

}