Q:

How to get reference to current Active window?

I want to get reference to currently Active window. For example, 1
Window above an application, how could I determine which
one is currently active?

A:

I got the answer on my own. See the following code to get the active window.
var activeWindow:NativeWindow = mx.core.Application.application.nativeApplication.activeWindow;
var parent:Sprite = (activeWindow.stage.getChildAt(0) as WindowedSystemManager).document as Sprite;

