what to use for cedar repair

Getting ready to put some Olympic oil-based transparent stain on my exposed 4x6 cedar rafter tails. Noticed a couple of the ends have holes; worst looks almost like a couple of 1" diam. holes drilled 3"-4" deep. When I cleaned them out, most of the loose material looked like dry wood powder, but surrounding wood seems solid. No sign of insects or mold. Recommendations what to use to fill the holes? Plan to use Olympic cleaner before staining. Fix holes before cleaning or after?
TIA
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Diane" writes:

May be carpenter bees.

I've seen Bondo or other fiberglass body repair putty used on wood siding, but that's for painted surfaces as it won't take a stain.
Marc
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Carpenter bees- they will return every year.

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