From the OP, IPC::Run3::run3 does not seem to work, I have included a working example below. (ActivePerl 5.10.1, IPC::Run 0.043) This will run the program in batch mode, which may or not work, or be what you want in your case.

use strict;
use warnings;
use IPC::Run3;

my (@fromme, @tome);

## Setup my input...
push @fromme, "3*12\n";
push @fromme, "40*4\n";

## Do it; running CLI calculator, but could be anything 
unless (run3( "bc.exe", \@fromme, \@tome, \@tome )) {
##                      STDIN     STDOUT  STDERR    ...for the program
  print "ERROR in command\n";
}


print "Return code = $?\n";

## Return output
while ($_ = shift @tome) {
  print "$_";
}

__END__
~~Output~~
Return code = 0
36
160
[download]

Maybe update your post with more detail of what you wish to do.

Good luck. -c