Hi Debbi: The fix depends upon your windows and how the sills are attached. For most double hung wood windows, the sill is an integral part of the window frame. To replace it requires removing the window from its opening. You do this by removing the casings, inside and out, then cutting off the nails holding the jam to the house's framing with a recip saw, then slide the window out. Once out, you can see how the sill is attached and how it can be replaced. In the past, I have simply made new sills using pressure treated lumber I plane, cut and shape to match the old one, then reinstall the window.
The most common causes of a rotting sill is because they were not made with enough of an angle cut on the exterior exposure thus not allowing rain water to run off the wood, they were not maintained with periodic scraping, priming and painting and/or weep holes were not installed in the base of storm windows, thus allowing condensation to build up on the sill as it ran down the windows in the winter time.