Not entirely sure I understand what you need, but if the idea is to avoid cross references being created, you might want to try $Data::Dumper::Deepcopy = 1;

For the following sample structure, the difference in output would be

my $y = { foo => "bar" };
my $X = { a => $y, b => $y, c => $y };

$Data::Dumper::Deepcopy = 1;

print Dumper($X);
[download]

$VAR1 = {
          'c' => {
                   'foo' => 'bar'
                 },
          'a' => {
                   'foo' => 'bar'
                 },
          'b' => {
                   'foo' => 'bar'
                 }
        };
[download]

while the default output (Deepcopy=0) would look like

$VAR1 = {
          'c' => {
                   'foo' => 'bar'
                 },
          'a' => $VAR1->{'c'},
          'b' => $VAR1->{'c'}
        };
[download]