Preheat your oven to 350 degrees.
Bring a large pot of water to boil.
Boil your pasta shells for about 10 minutes, or until cooked al dente. Rinse shells in cold water when they're done cooking, to stop them from cooking more. Set aside.
Meanwhile, in a large saute pan cook up your ground beef. Drain the grease from the pan and set the beef aside.
Add the onions and bell peppers and mushrooms to the pan and cook for 3-4 minutes until the vegetables start to get soft.
Mix the vegetables with the ground beef. Stir in the salt and pepper and the cream cheese, and mix thoroughly.
Pour about 1/3 of your Alfredo sauce on the bottom of a 9x13 in pan and spread around.
Fill each of your shells with a heaping tablespoon of your meat mixture and place into your prepared pan.
Repeat until all shells, or the meat mixture is gone.
Pour the remaining Alfredo sauce over the top of your shells.
Wrap pan in foil and bake for 30 minutes, or until the mixture and noodles are hot throughout.
Remove foil and top with cheese.
Return to oven and bake for an additional 15 minutes until the cheese is melted and bubbly.