# Traverse the tree and create a data array of unique     elements
  my $lastline;
  while($HList->info('exists', $Topology))
  {
    $_ = $HList->info('next', $Topology);
    $Topology = $_;

    unless (/^$lastline/) 
    {
      push (@data, $lastline);
    }
    
    $lastline = $_;  
  }
  
# Seperate the child from the parent (leaf from the tree)
my $cnt = 0;
foreach $_ (@data)
{
  if ($_ =~ /\//)
  {
    $check = $_;
    ($parent, $child) = $check =~ m/(.*\/)(.*)$/;
    # Only take the unique parents
    push (@master, $parent) unless ($seen{$parent}++);
    $child = join("", $child, "\=[Unique $cnt]");
    $cnt ++;
    push (@master, $child) unless ($seen{$child}++);
  }
}
    print "MASTER: @master\n";
[download]

I'm not seeing @master = () anywhere in what you posted, so it's still not clear what kind of problem you're acctually having.

And while it's not typically neccessary to include all of your code when asking a question, people do need enough to provdie context: in the case of your question, there's no clear indication what the $HList object is, or what $lastline is.

A good rule of thumb is to only post code that can be compiled/run by itself and will demonstrate the problem in it's output -- a standalone test case so to speak. In otherwords, take snippets of your "problem code", preface them by enough declarations and initializations to make it clear what types of data will be in your variables, and then put some print statementsafter your code that show the values in your variables after the problem code has run. This not only makes it possible for people on perlmonks to diagnoss your problems, but it helps ensure that the problem is where you think it is, and not caused by something you think is unreleated.

Frequently, creating standalone test scripts like this helps people find their bugs without even needing to post them.