We had a roof leak that ran down the window frame and got the window sill wet. Everything is dried out and the roof is fixed. Any ideas on how to fix this window sill? I'd prefer not to have to remove the sill and just peel off the paint and what seems to be joint compound or something? Could I skim a layer of wood filler after I peel off the damaged sections of the top layers? There is wood under the top layers. enter image description here

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That's probably just several layers of paint or paint plus a specialty undercoating for trim.

Chip it off, ensure there's no mold, remove any rot using a wood chisel, patch with a good quality wood filler, sand to 100grit or better, seal with a good primer/sealer, and repaint. If you find mold it's probably easier to just replace the sill, bleach and most mold killing products will not work on wood (including mold killing primer)

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