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<?xml version="1.0" encoding="ISO-8859-1"?>
<top xmlns:xi="http://www.w3.org/2001/XInclude">
...
    <xi:include href="$WORK_ROOT/MOD_B/module_b.xml"/>
    <xi:include href="$WORK_ROOT/MOD_C/module_c.xml"/>
</top>

<?xml version="1.0" encoding="ISO-8859-1"?>
<record xmlns:xi="http://www.w3.org/2001/XInclude">
...
                 <data>data</data>
        </module>
</record>

use XML::DOM;
use XML::SAX;
...
);
$parser->parse_uri($input_file);
close($output);

$parser = new XML::DOM::Parser;
my $doc = $parser->parsefile("$output_file");