Can you help me?
I need to be able to move to any point on the screen even if it is covered by the air application and click the mouse on an object that is on the background program.
I.e. application will be transparent with alpha 0.5 and user will be able to click objects under application.
Can it be done by Adobe AIR in Flash Builder?
No, I don't think this is possible. There is a threshold at which the application no longer intercepts mosue clicks, but it is around alpha = .05 (and is different for Windows and Mac).