# parsing File 1
my @nodes_from_file1 = $parser->findnodes('//Feature');
# or whatever it is you need in each node

# later
my $new = XML::LibXML::Document->new('1.0', 'utf-8');
my $features = $new->createElement( 'Features' );
my $file1 = $new->createElement( 'File1' );
for my $node (@nodes_from_file1) {
	$file1->addChild( $node );
}
$features->addChild( $file1 );
# and so on

##</code><code>##

<Features>
  <File1>
    <Feature>
		<Number>86839</Number>
		<Prefix>419</Prefix>
		<Alt>73924</Alt>
	</Feature>
    <Feature>
		<Number>82783</Number>
		<Prefix>826</Prefix>
		<Alt>27800</Alt>
	</Feature>
    <Feature>
		<Number>82783</Number>
		<Prefix>827</Prefix>
		<Alt>26433</Alt>
	</Feature>
  </File1>
</Features>