Insert the screwdriver through the rotten window sill to find out the extent of the rot. If the screwdriver goes in easily more than half an inch, then you must replace the sill. If the screwdriver barely goes in, you can repair it with wood epoxy.
Scrape off any rotted wood that is sticking out with the spatula. Only remove the rotted wood that is bulging out, compared to the rest of the window sill. Use the paint brush to brush off any dust or debris off the window sill.
Mix the wood epoxy. Mixing instructions vary by manufacturer, so follow the manufacturer's direction for the best mix.
Apply the mixed wood epoxy over the rotted window sill with the putty knife. Cover all holes and cracks on the wood until the epoxy is even with the rest of the non-rotted wood. To ensure the epoxy cures completely, let it dry overnight.
Remove excess epoxy and shape the epoxy with the wood rasp. So that the patch is even with the rest of the wood, lightly sand it with the sand paper.
Apply primer and paint to the window sill to ensure the wood remains waterproof. Read the paint can's direction for drying times between paint coats.