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    <p>What is your program supposed to be doing? Your current program is looking for the lines that have <code>matched pattern</code> and storing <strong><em>THOSE VERY LINEs</em></strong> into three different arrays. All other lines are ignored.</p> <p>You show some sort of example output, but there's no real relationship between your output and input.</p> <p>First, learn about <a href="http://perldoc.perl.org/perlreftut.html" rel="nofollow">references</a>, so you don't need five different arrays. In my example, I use an array of arrays to store all of your separate files. If each file represents something else, you could use an array of hashes or a hash of arrays or a hash of hashes of arrays to represent this data in a unified structure. (Don't get me started on how you really should learn object oriented Perl. Get the hang of references first).</p> <p>Also get a book on modern Perl and learn the new Perl syntax. It looks like your Perl reference is for Perl 4.0. Perl 5.0 has been out since 1994. There's a big difference between Perl 4 and Perl 5 in the way syntax is done. </p> <pre><code>use strict; use warnings; # Prints out your data strtucture use Data::Dumper; my $array_num; my @array_of_arrays; use constant { PATTERN =&gt; qr/matched pattern/, }; while (my $line = &lt;DATA&gt;) { chomp $line; next if $line =~ /^\s*$/; #Skip blank lines if ($line =~ PATTERN) { if (not defined $array_num) { $array_num = 0; } else { $array_num++; } next; } push @{ $array_of_arrays[$array_num] }, $line; } print Dumper (\@array_of_arrays) . "\n"; __DATA__ matched pattern 1 line1:10 line2:20 line3:30 next matched pattern 2 line1:5 line2:10 line3:15 next matched pattern 3 lineA:A lineB:B lineC:C </code></pre> <p>OUTPUT. Each set of lines are in a different array:</p> <pre><code>$VAR1 = [ [ 'line1:10', 'line2:20', 'line3:30' ], [ 'line1:5', 'line2:10', 'line3:15' ], [ 'lineA:A', 'lineB:B', 'lineC:C' ] ]; </code></pre>
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