I'm not sure I understand the question when read with the title. If you're looking to mask the password when entered on the command line, use Term::Readkey.

Your script with the Term::Readkey stuff inserted - I check to see if you have it installed first. Not sure if it is a core module. If not, then just install it, not a big deal.

use strict;
use warnings;

use Win32::OLE;
use Data::Dumper;
# use Term::ReadKey
my $HAVE_Term_ReadKey = eval {
    require Term::ReadKey;
    Term::ReadKey->import;
    1
};

## specify EFT connection information. If the eftadmin password change
+s, it needs to be changed here as well.

our $domain='OurDomain\\';
our $pass;
our $user;

CONNECTION: {

    print "Account ID? ";
    chomp (my $s_id=<STDIN>);
    $user=$domain . $s_id;
    print "  Using $user to authenticate.\n";
    print "Password? ";
    if ($HAVE_Term_ReadKey) { ReadMode(2) }
    chomp (my $pass=<STDIN>);
    if ($HAVE_Term_ReadKey) { ReadMode(0) }
    print "\n  Password: $pass\n";

    print "  CONNECTING TO APP ...\n";
    print "  CONNECTED TO APP ...\n";
    $pass = undef;
    print "Password: $pass\n"
}
[download]

The script outputs:

VinsWorldcom@C:\Users\VinsWorldcom\tmp> test
Account ID? vinsworldcom
  Using OurDomain\vinsworldcom to authenticate.
Password?
  Password: My_Password
  CONNECTING TO APP ...
  CONNECTED TO APP ...
Use of uninitialized value $pass in concatenation (.) or string at C:\
+Users\VinsWorldcom\tmp\test.pl line 34, <STDIN> line 2.
Password:

VinsWorldcom@C:\Users\VinsWorldcom\tmp>
[download]

Notice the "Password?" prompt has no text next to it as the ReadMode(2) call turns off echo so you don't see the user typing their password. It does get saved to $pass however. But also notice the "Use of uninitialized ..." error after "CONNECT..." because we set $pass to 'undef' and then print it - just so you see it has been "erased" after using it to authenticate.

Are you concerned that people will be snooping the memory of the computer you are running the script on while you're running the script - and thus need the obfuscation of the $pass variable immediately?