If I understand you right you want all <Module> tags into one file and all other tags directly in <Root><Top> into the other, right? This is what it could look like using XML::Rules:

use strict;
use XML::Rules;

open MODULE, '>', 'splitXML-test-Module.xml';
print MODULE "<Root>\n <Top>\n";

open OTHER, '>', 'splitXML-test-Other.xml';
print OTHER "<Root>\n <Top>\n";

my $parser = XML::Rules->new(rules => {
    Root => '',
    Top => '',
    Module => [
        '/Root/Top' => sub {
            my ($tag_name, $attrs, $context, $parent_data, $parser) = 
+@_;
            print MODULE '  ' . $parser->ToXML($tag_name, $attrs) . "\
+n";
            return;
        },
        'raw'
    ],
    _default => [
        '/Root/Top' => sub {
            my ($tag_name, $attrs, $context, $parent_data, $parser) = 
+@_;
            print OTHER '  ' . $parser->ToXML($tag_name, $attrs) . "\n
+";
            return;
        },
        'raw'
    ]
});

$parser->parse(\*DATA);

print MODULE " </Top>\n</Root>\n";
print OTHER " </Top>\n</Root>\n";

__DATA__
<Root>
 <Top>
  <Module name="ALU">
   <input name="po_ctrl"/>
   <bidirection name="add"/>
  </Module>
  <Module name="Po_ctrl">
   <input name="ctrl"/>
   <output name="ctrlbus"/>
   <bidirection name="add"/>
  </Module>
  <input name="add"/>
  <input name="clk"/>
  <input name="da_in"/>
  <output name="da_out"/>
  <bidirection name="ctrl"/>
</Top>
</Root>
[download]

Basically you specify that you do not want to "return" anything from the <Root> and <Top> nodes, that the <Module> tags directly under <Root><Top> should be printed (including attributes and content) into the MODULE filehandle and otherwise just remembered for the parent tag. That other tags if directly under <Root><Top> should be printed to the OTHER filehandle and otherwise remembered.

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