There are all sorts of ways to protect wood from clamps. Unfortunately, most would be easier to accomplish if you had three hands.

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Coat the business end of your clamps with the plastic-dip material marketed to coat tool handles. It dries to a soft, flexible coating that will protect even finished wood. Apply it by dipping or brushing, taking care to keep it out of movable joints or threads. Coat the grip end of a pair of pliers or locking pliers, too, to make a handy tool for pulling out wooden axle pegs and the like.
—Raymond Babcock, San Angelo, Texas