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#!/usr/bin/perl -w
use strict;
...
foreach my $foo (@fields) {
  print "$foo->[2]\n" if ($foo->[2] != 3);
}

  push @Array , [ @Fields[0,3,6] ];
}
...
foreach my $foo (@fields) {
  print "$foo->[2]\n" if ($foo->[2] != 3);
}

while (<FILE>) {
  next if (/^#/);
...
  chomp $Fields[6];
  push @Array , [ @Fields[0,3,6] ];
}

chomp @Array;