my $username;
my $password;
print "Please enter username to connect to the system:" ;
chomp($username=<>);
print "Please enter password\n";
chomp($password=<>);
[download]

I think you you are getting what you want, but your printout statement is misleading you?

#!usr/bin/perl
use strict;

my $in = 'r;OFTaf#a2Mt9d\1'; 
         #single quote is literal quote
         #this is what your input should get
print $in, "\n";
          #print $in "as is", not within quotes

=prints
r;OFTaf#a2Mt9d\1
[download]

a script to login to another system via ssh

Don't mess with passwords, use public key authentication. See PuTTY FAQ "Remember Password" and Using public keys for SSH authentication. (Note that using public key authentication is not PuTTY specific, it's a basic feature of SSH.)

Alexander

--
Today I will gladly share my knowledge and experience, for there are no sweeter words than "I told you so". ;-)

I have some quibbles about how you accept input. In a standard command line I/F leading or trailing spaces should not matter. But this looks to me like it should "work". How are you printing $password?

I don't know what the rest of your code does.
Code like this should get the input token and strip out the leading and trailing white-space.

#/usr/bin/perl
use warnings;
use strict;

my $username;
print "Please enter username to connect to the system:" ;
$username=<>;
$username =~ s/^\s+//;  #trim leading whitespace
$username =~ s/\s+$//;  #trim trailing whitespace
                        #this includes \r, \n, etc.
print $username, "\n";
[download]