use Win32::GuiTest qw(FindWindowLike SetForegroundWindow SendKeys);
system("start p.bat");                 # start ensures that the program opens in a new window
sleep(1);                              # give p.bat a chance to load
my @win = FindWindowLike(0, "^p.bat"); # find p.bat's window (maybe more than one)
SetForegroundWindow($win[0]);          # bring the first p.bat window to the foreground
SendKeys("y");                         # send a keypress to the active window in this case a "y"
__DATA__
For this example, p.bat contains one line:
pause