foreach my $msgid (@heads) {
    # do what ever you have to do to start a new thread
   
    # recursively follow the messages
    thread_msgs($hash{$msgid});
}

# recursively read through the thread
sub thread_msgs {
    my $msgid = shift;

    # use seek() to position the mbox file at
    # the message start using $msgid->{filepos}
    # copy to the end of the message

    foreach $msgid (@{$msgid->{nextmsg}}) {
        thread_msgs($msgid);
    }
}