Try adding this code to your themes functions.php file,
function __custom_messagetypes_link( $link, $term, $taxonomy )
{
if ( $taxonomy == 'plugins' ){
return str_replace( 'plugins/', '', $link );
}
else if ( $taxonomy == 'themes' ){
return str_replace( 'themes/', '', $link );
}
else{
return $link;
}
}
add_filter( 'term_link', '__custom_messagetypes_link', 10, 3 );
I am assuming the used slug, May be you have to change the your taxonomy slug if these are different.
If have any problem you can freely ask, Thanks,