Cut off mushroom stems, coarsely chop, and set aside. Arrange mushrooms skin side up on a cooking spray coated baking sheet. Cook for 15 minutes.
Heat a cooking spray coated frying pan over medium heat. Cook mushrooms stems, peppers, shallots, green onions, and garlic 8 to 10 minutes or until soft. Mix in basil, marjoram, and thyme and cook 1 to 2 minutes. Sprinkle with salt and pepper.
Spoon vegetable mixture into mushrooms and top with cheese. Cook mushrooms in oven 10 minutes or until cheese melts. Top with basil.