Prescription medications my include anti-inflammatory medications such as Kenalog in orabase, or soothing mouth rinses for comfort. One I use a lot for really bad cases is a mixture of Benedryl liquid, viscous xylocaine, and maalox, all mixed together. Seems to help in some cases when there are multiple lesions. I have even seen some people use silver nitrate sticks to basically burn the lesions-hurts a lot at first but some say it helps the pain. ( I don't recommend this). As with all lesions a proper diagnosis is very important. You have to determine if it is something else. One basic guideline is, if it doesn't go away in 2 weeks, you get suspicious of other things.
Link: Canker Sore/Mayo Clinic