You can programmatically close windows if you know their handles. Here are two non-tested examples.

use Win32::GuiTest qw/SendMessage/;
use Win32::FindWindow;
$window = find_window( basename => 'winword.exe' );
SendMessage($window->hwnd,WM_CLOSE,0,0);
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OR

use Win32::CtrlGUI;
my $window =Win32::CtrlGUI::wait_for_window(qr/Word/);
$window->send_keys("!fx");
my $window =Win32::CtrlGUI::wait_for_window(qr/Excel/);
$window->send_keys("!fx");
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HTH,
SSF