You should not smoke while you are wearing your Invisalign trays still in because it can cause discolouration and stain your teeth.  If tobacco ends up getting into the tray it can even cause tooth decay.  If you are going to smoke after removing your Invisalign aligners it is a good idea to brush and floss your teeth once you are done to reduce your risk of tooth discolouration, and gum disease later on in life.