Cut spaghetti squash in half and remove all the seeds.
Drizzle the inside of the squash with olive oil and rub to cover the inside of the squash. Sprinkle with salt and pepper.
Place squash halves, cut sides down, in an 8x8 casserole dish; add the ¼ cup water. Microwave, covered, on high for 15 minutes. Or until tender.
While the squash is in the microwave, start working on the Alfredo sauce. In a medium saucepan over medium heat, place the cream cheese and butter. Once melted, slowly incorporate the heavy cream and ½ cup of Parmesan cheese. Once well combined, whisk in the garlic, pepper and nutmeg. Set to low heat and whisk occasionally.
Once your spaghetti squash is tender, cool slightly and separate strands of squash with a fork. Spread the strands evenly onto the same 8x8 dish you cooked it in. Evenly pour the Alfredo sauce over the top of the squash stands.
Top with the mozzarella cheese and ¼ cup of Parmesan cheese and place uncovered in the oven under broil until cheese is slightly browned and bubbly (about 3-5 minutes)
Garnish with fresh thyme or parsley