Here is what I would do (code snippets untested):

• Open the first file
• Iterate through the file, building a hash making each line a key, eg:

  # assumes that duplicates in first file should be ignored.
  my %wanted;
  open my $in, '<', '$file1' or die "$!\n";
  while (my $line = <$in>) {
    chomp $line);
    $wanted{$line}++;
  }
  [download]

• Open the second file
• Iterate through it line by line
• Extract the second "field" from each line using split

  my $foo = (split /|/, $line)[1];
  [download]

• If this value exists as a key in the hash you built earlier, print the record to your third file

  print OUT $line if $wanted{$foo};
  [download]

This may not be the fastest approach, but it does only open and read each of your input files once. As opposed to 60,000 X 16,000,000 = 960,000,000,000 times - which is what your current code does.
So I'd expect it to be just a tad faster ;)

Hope this helps,
Darren :)

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