A kitchen counter was a flat surface in a kitchen where food could be prepared.
Germs could survive on many different surfaces, including kitchen counters. In 2151, as part of his answer to Gabrielle Witty's question about whether germs could live in space, Doctor Phlox gave several examples as to where they could live, including kitchen counters. (ENT: "Breaking the Ice")
In 2372, Neelix recalled to B'Elanna Torres that he once fell asleep at the counter after becoming exhausted while trying to perfect his Jibalian omelette. (VOY: "Prototype")