Where wood sills or sash have taken serious abuse from weather, resulting in rot, you can use epoxy wood filler, available at home centers, to repair the area. (If large areas are affected, talk with a carpenter or cabinetmaker about replacing sections of the wood or the entire sash.) Contact a window replacement or repair contractor if you need help.
Here's how to fix the problem yourself: 1) Use a chisel to dislodge most of the loose, rotted wood. Drill a few 1/4-inch holes into the damaged wood.
2) Soak the entire rotted area with liquid epoxy “consolidant” to transform the area into a sturdy base for filler. Let the wood absorb it for about five minutes and then reapply, wait, and reapply until the wood ceases to accept consolidant.
3) Knead a batch of epoxy filler according to label directions and mold the repair. As the material cures, dip a putty knife in solvent and use it to sculpt and shape the repair.
4) Sand, file, or rasp as needed, and paint the area within three days.