To create custom-fit mouth trays, your dentist will take an impression of your teeth and then have exact molds made of your tooth arches (upper, lower or both). At home, you'll fill these trays with the specified peroxide solution in the manner your dentist directs - usually minutes or hours every day for up to two weeks.
Some over-the-counter kits may also feature custom-fit trays, although since you'll be taking the impression yourself, you should be aware that the match might not be exact. More than likely, though, kits you purchase yourself will contain either BOIL AND BITE MOUTH TRAYS or STOCK or ONE-SIZE MOUTH TRAYS.
"Boil & Bite" trays offer some customization to enhance bleach-to-tooth contact. They're made of a malleable substance that, when gently heated and applied directly to teeth, conforms to the shape of your own mouth. Stock or One-Size Mouth Trays are exactly as they sound - inexpensive plastic shells that fit the general shape of average upper and lower arches. In addition to their lack of exact fit, stock mouth trays are often also made with a thicker type of plastic than their custom or boil & bite counterparts. Thicker walls in turn may add to discomfort, increase salivation (which further dilutes the whitening agent) and interfere with bite patterns.
Still, when comparing results to cost, many consumers find that they're satisfied with the whitening effects of self-purchased kits, especially since they're generally less expensive than those kits prescribed by regular or cosmetic dentists.
From : http://www.teethwhiteningreviews.com/artman/publish/all-about-teeth-whitening-trays.php