Well there is always the Abort VI Invoke method that can be called. But, that's not the best way. How would you usually close that VI? Is there a stop button? You can access that by get a list of all controls of the VI.
You can close the reference and it'll be removed from memory IF there are no other demands on it. Read the help file on Close Reference Function for details. Like the abort function this acts somewhat like the stop sign so you need to be careful with it. Other options are queues, notifiers, global variables, functional globals, shared variables.