How Does One Clean Invisalign?

Invisalign trays are clear so you can easily see any food or discoloration. This allows the trays to be easily cleaned because you always know if you have more work to do.
I recommend using a toothbrush with water and making sure you clean ALL of the nooks and crannies. Remember, your teeth have hills and valleys which come together to allow you to chew. Your aligners have all of these same hills and valleys, as the trays are manufactured specifically for your teeth down to the slightest detail. This means that you should get in there and clean every aspect, or the trays will gradually start to discolor, making them more noticeably to friends and peers. Simply cleaning them with a toothbrush and water - but being meticulous while doing so - can make them spotless and remain spotless. 
I do not recommend using toothpaste when cleaning the trays, because toothpaste has tiny abrasives, which over time can make the trays appear less pristine and clear. Excessively brushing the trays with toothpaste can actually give the trays a more "cloudy" look - making the trays more noticeable.

Cleaning Invisalign aligners is very simple. Every time you brush your teeth, you should gently brush your aligners (on the inside and outside) and rinse them in lukewarm water. You can also soak them in a denture cleaner, or with Invisalign cleaning crystals while you are eating. Most importantly, make sure you brush and floss after each meal, so that food and saliva doesn't get trapped in the aligners and soak into your teeth.