Use pmpro_levels_array filter to remove specific levels from your levels array. In this case, we are removing Free levels, leaving only paid levels to be returned to your PMPro levels array.

my-pmpro-levels-array.php

/**
 * The function my_pmpro_levels_array is an arbitrarily named function, which
 * you can rename to something more meaningful, as long as it is uniquely 
 * named on this site.
 * 
 * @param  array $levels Input the array of levels from your site
 * @return array         Output all paid levels, ie NOT the free level(s)
 */
function my_pmpro_levels_array( $levels ) {
	$newlevels = array();

	foreach ( $levels as $level ) {
		if ( ! pmpro_isLevelFree( $level ) ) {
			$newlevels[] = $level;
		}
	}

	return $newlevels;
}
add_filter( 'pmpro_levels_array', 'my_pmpro_levels_array' );