I think you want something like this (untested):

my $dir = 'C:/Documents and Settings/mydir/Desktop/current/Test_Files'
+;
open my $out, '>', "$dir/data.txt" or die "can't open out file: $!";
opendir my $dh, $dir or die "can't opendir $dir : $!";
while(my $f = readdir($dh)) {
  next if ($f eq 'data.txt');
  open my $fh, '<', "$dir/$f" or die "can't open file $f : $!";
  my $first_line = <$fh>;
  while (my $line = <$fh>) {
    chomp $line;
    my ($well,$sample,$barcode,$block_id) = split(/\t/, $line);
    my $name = substr($block_id, 11);
    $sample =~ /(\d+)(.*)/;
    print $outfile "$well\t$1\t$2\$barcode\t$name\n";
  }
  close $fh;
}
closedir $dh;
close $out;
[download]

Notes:

• readdir lets you loop over all the files in a directory, but you still need to open and read each file.
• It's not good to write your output into the same place all your input files are - your script will try to read it too!
• Be careful using the special variable $_ - this is the "default" output of many operations, so it's easy for one to clobber another. I like to store lines read from a file into a variable, just to be safe.
• The special variables $1 and $2 (regex matches) are also easy to clobber (what if you add another regex to your script sometime in the future?) So either store them in other variables right after the regex, or else use them immediately.

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