Preheat your oven to 350°F.
Make your pasta according to package directions, in a pot of boiling, salted water. Strain and set aside in the same pot.
Melt the butter in a medium pan over medium heat.
Whisk in the flour. Whisk continuously for 2 minutes. The mixture (roux) should be bubbling by now.
In one continuous stream, slowly add the milk, all the while whisking continuously.
Once all the milk is added stir frequently until the sauce has thickened enough to coat the back of a spoon (about 7-10 minutes).
Now, add your cheese to the sauce, about ⅓ to ½ cup at a time. Stir, and allow the cheese to melt in between additions.
Once all the cheese has been added, add the salt, pepper and nutmeg. Stir to combine. Next, pour the cheese sauce over the cooked pasta.
Pour the pasta into a 9x13" baking dish, and make the topping.
Combine the panko, olive oil, thyme, garlic, and parmesan in a medium bowl and mix with your hands. Spread evenly over the mac and cheese.
Bake at 350°F for 30-40 minutes, until bubbling and the panko crust is golden.