Right, here's what we're saying:

my @array1;
my @array2;

my @args = (
    [ \@array1, "foo", "file_1.gz"],
    [ \@array2, "bar", "file_2.gz"]
);

foreach (@args) {
    &file_processing($args->[0], $args->[1], $args->[2]);
}

sub file_processing {
      my ($array_ref, $arg, $file) = @_;
      my $script = "/export/home/ssesar/Perl/another_script.pl";
      open(FILE, $script . ' ' . $arg . ' ' . $file . ' |') or die ("c
+an't do it: $!\n");

      while (<FILE>) { 
          chomp;
          push @{$array_ref}, $_ unless /^(?:\#|none|unknow)/i;
      }
      close FILE;
  }
[download]

This should do what you want as best as I can tell -- open a file and push into an array (either array 1 or array 2 depending on which iteration) any line that doesn't start with UNKNOW/unknow/#/NONE/none.

Your lines

@_ = split ( /\n/, $_);
@array1 = @_;
[download]

look very strange -- as someone else pointed out, if you're reading in the file line by line (which is what <FILE> implies) then the final split on \n is useless.

In addition, you're only assigning the last value of @_ to @array1 (meaning the other values are lost) unless you've undefined $/, in which case you should just use my $file = <FILE> rather than the while loop.

Hope this helps.