Preheat oven to 400ºF. Mark a small X in the bottom of each tomato. Bring a small pot of water to boiling, submerge tomatoes for 20 seconds, and then immediately transfer the tomatoes to a bowl of ice water. Remove skins from tomatoes and place on paper towel to absorb excess water.
Lay puff pastry sheet on lightly floured surface. Slice sheet into thirds lengthwise, then cut each third in half. Cut each half into sixths, yielding 36 equal size puff pastry squares. Place squares 1” apart on a parchment paper-lined baking sheet and bake for 10 minutes.
Meanwhile, slice the very top and bottom off the tomato, and then slice each one into six equal round slices, totaling 36 slices.
Remove puffed squares from oven and place a slice of tomato on top of each and then top with a slice of cheese.
In a small bowl, mix together thyme, garlic powder, extra-virgin olive oil, and a pinch of black pepper and drizzle 1/4 tsp. on top of each mini pizza.
Return to oven until cheese just softens and tomatoes are heated through, about 2-3 minutes. Serve immediately.