Another thing you can do is use concatenated keys rather than a multidimensional data structure. (I don't know how critical the hierarchical nature is to your problem solution) That is, instead of:

$data {$a}{$b}
$data {$a}{$b}{$c}
$data {$d}{$e}
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you would use

$data{join "\0", $a, $b}
$data{join "\0", $a, $b, $c}
$data{join "\0", $d, $e}
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Then to access the keys you'd use your standard keys operator:

for (keys %data) {
   # you could do something with $data{$_} directly,
   # or if you need access to the individual keys ...
   my @keys = split /\0/;
   # ...
}
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The main caveat is that your "key separator" should be something that doesn't appear in your keys. I chose "\0" in this example assuming that your keys aren't likely to contain NUL bytes.