#!/usr/bin/perl -w
use Data::Dumper;

{my $i=1;
sub makevalue {
  return $i++;
}
}

my $hash={};my $h0;
my $l;my @c;
while ($l=<DATA>) {
  $h0=$hash;
  @c=split '/',$l;
  for my $c (@c[0..$#c-1]) {
    next unless $c;
    $h0=($h0->{$c}||={});
  }
  $h0->{$c[-1]}=makevalue($l);
}

print Dumper($hash);

__DATA__
/root/dir1/file1
/root/dir1/file2
/root/dir1/file3
/root/dir2/file1
[download]

Outputs:

$VAR1 = {
 'root' => {
   'dir2' => {
     'file1' => 4
    },
    'dir1' => {
      'file2' => 2,
      'file3' => 3,
      'file1' => 1
    }
  }
};
[download]

What does it do: it splits each row, and walks down the HoH (creating empty hashes as needed), putting the computed values (in this example just a counter) on the leaf.

I think this is more or less what you were describing, but I can't come up with a better solution.

-- 
        dakkar - Mobilis in mobile