Preheat oven to 375°F (190°C). Place tortillas on an ungreased baking sheet, and prick all over with a fork. Brush melted butter on top of each tortilla (leave some for sauteing veggies).
Bake for about 5-7 minutes, until puffed and just golden brown. Remove from oven and let cool.
In a large skillet, heat the remaining butter over medium heat. Add the sliced onions and pepper and cook over medium-low heat, stirring occasionally, until translucent and caramelized (about 7-8 minutes). Remove skillet from heat.
While onions and peppers are cooking, brush enchilada sauce over each of the baked tortillas. Top with sauteed onions and peppers,chicken, tomatoes, and sprinkle with cheese.
Place is back in the oven and cook for 4-5 more minutes, until the cheese has melted. Remove from oven and garnish with fresh cilantro, sour cream, and/or salsa. Enjoy!