You should always clean your clear retainers before putting them back on your teeth. That means after you brush your teeth in the morning and in the night, and it means after you have taken them out to eat or drink. You do not want to trap any food or debris in there just to settle on your teeth!
The first thing you should do when cleaning your clear retainers is to rinse them with water. When doing so though, make sure you do not use hot water. That high temperature can end up distorting the shape of your retainer, which means it will not be as effective as keeping your teeth in place. Rinse only with cool or lukewarm water.
To brush your aligners, use a soft-bristled toothbrush in small circular motions. Remember to clean both the inside and outside of the retainer to make sure you are getting away all the bad bacteria that may be hiding there. Use liquid dish soap instead of toothpaste on your retainers. Once you are done, go ahead and give it another rinse.