Lay one (1) sheet filo dough on paper and brush lightly with a little melted butter. Sprinkle all over with 1 tablespoon parmesan cheese. Repeat layering five (5) more times (with filo, butter, and parmesan cheese), pressing each sheet firmly so it sticks to sheet below. Lay the last filo sheet on top, brush with remaining melted butter, and sprinkle on remaining 1 tablespoon parmesan cheese.
Scatter onion slices across filo, top with mozzarella cheese, and arrange tomato slices in a single layer, overlapping slightly. Sprinkle with thyme or basil and salt and pepper to taste.
Bake until filo is golden brown, approximately 30 to 35 minutes. Remove from oven and let cool 10 minutes, then serve.
Serves many as an appetizer - Makes about 20 3-inch squares.