Bring a large pot of salted water to a boil. Add the 3 cups of elbow macaroni and cook according to the package directions, until al dente. Drain through a strainer, and set the cooked macaroni aside.
Add 1 cup cauliflower, 1 cup butternut squash, and 1 cup carrots to a steamer or large pot with enough water to cover them. Let the vegetables steam or boil until they are tender when poked with a fork. Drain the vegetables from the water.
Add the cooked vegetables and 1 cup milk to a blender or food processor and puree until they are smooth and creamy.
Pour the pureed vegetable mixture into a medium saucepan over medium high heat. Add in 2 cups shredded cheddar cheese, and 4 oz cubed softened cream cheese. Stir together. Let everything simmer and stir frequently until all of the cheese melts (The cheese will melt much faster if the cream cheese is cut into cubes).
Once the sauce is smooth and creamy, add the cooked macaroni to the pot and mix everything together. Scoop into bowls and serve with your favorite toppings or sauces.
