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";
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