Using a sharp paring knife, cut out the cores and seeds, lightly scrap out some of the inside of the apple with a small spoon, keep bottom of apples intact.
Place brown sugar, cinnamon, pecans and flax seed in a small bowl. Stir to combine. Fill each apple with brown sugar mixture. Put apples in a baking dish. Place a quarter piece of cream cheese on top of each apple, then dot each apple with a quarter piece of butter.
Pour boiling water in bottom of baking dish. Bake at 375º for 30 to 45 minutes and apples are cooked through and tender. Remove apples from oven.
Drizzle baked apples with caramel-butterscotch ice cream topping.