If you'd like to eliminate your freckles the high-tech way, lasers will do the trick. Freckles are melanin, and melanin absorbs the spectrum of laser light. The laser light negates the freckle, leaving just the keratinocyte cells beneath. Generally, a doctor (usually a dermatologist, cosmetic surgeon or general practitioner) will use a ruby- or green-colored, low-powered "Q-switched" laser light to blast away each freckle. This process is called fractional resurfacing, or it's know by its brand name, GentleLASE.
Since freckles are located at the very top level of the skin, the procedure is not invasive, and the laser won't damage any tissue on its way to the freckles. However, since it's a laser burning things off your skin, the process may cause irritation. After-effects include crusting and minor bruising. Your doctor may apply a topical cream to minimize discomfort.