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The rot could also be from the window sweating and condensation.

Depends on the material that the stool is made of. If it is wood, it could be cut out, patched, and re-painted. That is probably the easiest way if the moisture source was temporary.

If you have some carpentry skills and the stool is wood, you can get some stool board and re-cut and install a replacement.

If we are talking about a drywall return/sill, the advice would be similar to the first advice (dig out, clean up, patch, sand, prime, paint).

If you can post up a picture, you will get more directed feedback.

I am not sure if you are talking about the exterior or interior of this window. If it is the interior you may be better off replacing the sill. If it is the exterior I have had success with a product made by Minwax called wood hardner it the basic shape of the sill is still close to original and the wood is just soft or has minimal deeper damage. The Minwax product is basically an easier to find version of the ones used to restore boats and can be found at most paint stores or the Big Box stores.

You should wait untill the sill is as dry as you can get it by waiting for good weather and possibly cover it loosly with plastic covering it on top but not sealing in the moisture by leaving the lower part open. Once you have a dry area to work with dig out any very soft areas and then you either brush the hardener on out pour it on to the damaged area. I do as many coats as I can to totally saturate the wood. Minwax also has a epoxy based filler much like wood colored body filler that you can use to fill the deeper damaged spots.

I have used this product often on older homes where the mouldings are no longer available and I have used it for interior repairs as well. In my area we have many older historic homes and the cost to have a mill make replacement profiles in small quantities prohibitive unless they happen to have the cutting heads from a previous job.

Don

If you search for Minwax wood hardener on Amazon.com, you will find a number of other brands too. The liquid ones are basically a sealer-filler - the 2 component epoxy ones and the Bondo wood paste/wood filler types are more like the body filler used on cars, and require mixing a small amount at a time, with a limited (5-10 minute) working time typically. The sealer/hardener is more for softened wood that still retains its shape as mentioned in the prior comment - the bondo type fillers are for filling in holes where you have dug or drilled or cut out bad wood. They can be shaped with a dremel tool, utility knife, sandpaper, etc to as close to the original profile as you want to take the time for.

With all these products, be sure to leave several days ddrying time, as the chemical outgassing can lift paints or stains put over them.

If you are not going to be painting the repair, be sure to check color - some of these are brightly colored so you can see where you did it, but will not cover with a stain. The clear and light colored ones you can usually sand rough, then stain with a couple of coats of a heavy-body oil based stain and get good coverage - not as perfect as replacing the wood strip entirely, but then who looks close at the finish on a window.