Preheat oven to 375 degrees. Lightly butter 6 standard muffin cups.
Cut tortilla with knife into 6 slices, put edges together placing it inside each muffin cup, cut out bottoms for cup with cookie cutter.
Slice ham into ling thin pieces. In a large skillet, cook ham over medium, until almost crisp.
Lay cheese, few ham slices in each tortilla cup and crack an egg over each.
Sprinkle with diced green onions and tomatoes. Season with salt and pepper.
Bake until egg whites are just set, 20 to 25 minutes. Run a small knife around cups to loosen.