1. Preheat the oven to 400 degrees F. On a baking sheet, place parchment paper or a silpat mat on top of the pan.
2. Grate the cheese (or use pre-shredded) of your choice of cheese. Measure out 2 tbsp. of cheese per shell. Spread the cheese out slightly onto the parchment so it's about a 3" circle. I suggest only doing 6 at a time. This makes it easier to form the cups before they cool.
3. Bake for about 7-10 minutes. The cheese should be browned slightly around the edges and look fully melted.
4. Remove from the oven and let sit on the baking sheet for 30-45 seconds. Use a spatula to remove from the parchment and place over a muffin tin. Carefully press it into the tin to form a "cup" shape. They do not need to be perfect. If the sides slightly bend in, this is ok too. Please be careful and work quickly. They can harden and cool fast!
5. Once the cups are made, work on the filling. Saute the onions in 1 tbsp. of butter till tender and translucent (about 5 minutes). Add the garlic and cook till fragrant.
6. Add the onion and garlic to the softened cream cheese. Stir to combine and season with salt and pepper to taste. Place in a piping bag or plastic bag to help pipe into the cups.
7. Saute the mushrooms, Worcestershire sauce, and fresh thyme in the remaining 1 tbsp. of butter. Cook till brown. Season with salt and pepper.
8. Pipe about a tablespoon of the filling into each cup. Top with a spoonful of mushroom (if there is excess liquid, try to avoid transferring this to the cups or they may get a little soggy).
9. Garnish with more fresh thyme and grated cheese if desired. Serve warm.