Not a wise move to fill those rocker panel holes. I assume you are asking about the ones that are fore and aft on each side of the car. These are the mounting "slots" for your jack. They should have a black plug in them. If the plugs are missing, clean out the mounts with a round wire brush and get replacement plugs.
Welcome to the forum and tell us more about your car.
I have an 88 300E, What are the holes in the rocker panel for? what would happen if I plugged them and shaved them closed permanently?
If you mean the two holes on the lower part of the cladding, one toward the front wheel and the other toward the rear wheel, then they should be plugged with the appropriate inserts.
These are the access areas to the jacking points of the car.
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