This was an idea from Don Fogg's website and I've used this method ever since the first time I tried it. It will prolong the lifetime of your stencils significantly over the old standby "run it under water and rub between your fingers with some soap".
The very best way I have found to clean stencils is with a sonic jewelry cleaner. If you go to a discount place like a Big Lots, you can usually find them for cheap. They typically come with liquid soap and a soft small brush. Use a small amount of soap in the sonicator with some luke warm (NOT hot) water and let it run for about ten mintes. You can use the brush VERY lightly to dislodge anything stubborn, but you have to be sure not to scrub or it will erode the edges of the letters. Then, rinse in tap water and pat dry.