As anonymonk points out there is no need to create the parsed elements from scratch: 
# 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

[download]
Using your sample data (which has errors btw) this would produce: 
<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>

[download]

In reply to Re: copy XML elements from one file to another by tangent
in thread copy XML elements from one file to another by Anonymous Monk

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