or die "File does not exist: $!";
I would change that to or die "Can't open 'counter' for reading : $!";

I would also change all that while business to

my @my_a = <PLAIN>;
[download]

1. How can i open and read the file in byte mode?

`perldoc -f open' should've told you about binmode.

2. How do we ensure that the @my_d == @my_a after we XOr it back? (i've tried it, but it mess up lots of whitespace)

Go ahead and show what you've tried, it could clear up what you're attempting to accomplish

Because this is a Crypto-Counter Mode process, do anyone know whats the simplest way of calling them? (rather than recreating these codes above).

Calling who? XOR is not crypto