To make a pop-up window from a subVI you go to VI Properties (pop-up on the icon form the front panel). Under the category: Window Appearance select Customize... In the dialog which appears check "Show front panel when called" and "Close afterwards if orignally closed." Save the subVI and close its windows. When you run the main VI, the subVI front panel will open and the user can interact with it until it finishes at which time it will close. If you do this you should also uncheck several other buttons like Show Abort and Allow user to close and probably some others.
Lynn