Scrape off any rotten wood with the end of a chisel. You may need to remove some of the wood by hand. Clear out the rotten area completely.
Dry out the rest of the wood sill with a hair dryer. Sealing in wet wood will re-create the same problem. Run a hair dryer over the wood until it is dry to the touch.
Coat the wood with an epoxy sealant. This will help prevent any future rot from occurring. Use a paintbrush to apply the sealant. Let it cure for at least 24 hours.
Fill in the missing areas of the wood with wood filler. Do not use a powdered wood putty or regular wood filler for this application. You need a liquid filler that will penetrate into the area and create a strong seal. Squeeze the filler out of the applicator, and fill in the area. Let it set for 24 hours. Examine the wood again. If you need more filler, apply a second coat, and let it cure.