Note that your code assumes that both files have the same number of lines, and that those lines have the same number of characters. To avoid that assumption, read in blocks with the read function instead of reading a line at a time. You should also use binmode, as PodMaster sggested.

Also, you may find that Crypt::CTR does some or all of what you want.

Something like this is a shorter way to do what you want. You can check they're equal with the string equality operators (eq and ne), as shown below.

# Read in
my @my_a = <PLAIN>;
my @my_b = <CTR>;

# XOR
my @my_c = map { $my_a[$_] ^ $my_b[$_] } 0..$#my_a;
my @my_d = map { $my_b[$_] ^ $my_c[$_] } 0..$#my_b;

# Check
foreach (0..$#my_d)
{
  $my_d[$_] eq $my_a[$_]
    or die "d[$my_d[$_]] != a[$my_a[$_]] at line $_\n";
}

print "OK\n";
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