XY problem question here...
What are you going to be using those arrays for? Are they huge, or is the sample/good a small subset of the input data? There may be better ways to approach the entire task.

Perhaps consider something more like this:

use strict;
use warnings;


open my $ifh, '<', 'test.pl' or die;
open my $ofh_samples, '>', 'samples.txt' or die;
open my $ofh_good, '>', 'goodlines.txt' or die;

$|=1;
my $total = -s 'test.pl';
my $progress = 0;
my $linecount = 0;

while (my $line = <$ifh>)
{
  $linecount++;
  $progress += length ($line);

  print $ofh_samples $1 if $line =~ /^sample\s+(\S+)/;
  print $ofh_good $1 if $line =~ /^good\s+(\S+)/;

  printf "Processing... %3.1f%% completed...   \r", 100*$progress/$tot
+al unless $linecount %100;
}
[download]

That will keep little more than one line in memory at a time, and you can then deal with the pieces separately. Uncomment the comments to give a progress display.