Why don't you create tag handlers for "thread" and "node" that build up your hierachy?

Here something to get you started

#!/usr/bin/perl
use strict;
use warnings;
use XML::Twig;
use Data::Dumper;

my %result;

my $thread= new XML::Twig(
    twig_handlers => {
        thread => \&thread,
        node => \&node,
    }
);

$thread->safe_parse(join('',<DATA>));
print Dumper( \%result );

sub thread {
    $result{$_->{'att'}->{'id'}}= childrenhash($_->children( 'node' ))
+;
}

sub node {
    $_->set_att( structure => { $_->{'att'}->{'id'}, childrenhash($_->
+children( 'node' ))} );
}

sub childrenhash {
    my %result;
    foreach my $child (@_) {
        my $ch= $child->{'att'}->{'structure'};
        @result{keys %$ch}= values %$ch;
    }
    return \%result;
}

__DATA__
<?xml version="1.0" encoding="ISO-8859-1"?>
<thread id="504929">
<node id="504941">
</node>
<node id="504942">
<node id="504950">
<node id="504964">
</node>
</node>
<node id="504953">
</node>
</node>
<node id="504944">
</node>
</thread>
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