To protect your treatment, you must take care of your aligners and keep them clean throughout the process. Luckily, keeping your Invisalign clean is simple and adds only a few minutes to our daily routine. Whenever you brush and floss your teeth every day, you should remove your aligners. After you’re finished cleaning your teeth, use your toothbrush and warm water to scrub every side of your aligners. This will keep your aligners clean and prevent harmful bacteria from living on your appliance.