I think i found a solution. Edit wp-admin/wpmu-edit.php
Find
if( constant( ‘VHOST’ ) == ‘yes’ ) {
$newdomain = $domain.”.”.$current_site->domain;
$path = $base;
} else {
$newdomain = $current_site->domain;
$path = $base.$domain.’/’;
}
Replace
$newdomain = $domain.”.”.$current_site->domain;
With
$newdomain = $domain.”.mydomain.com”;
Let me know if there anything wrong in doing this.