Preheat oven to 375 degrees. Finely chop pine nuts in a food processor; transfer to a small bowl, and stir in cheese. Lay one phyllo sheet flat on a clean work surface. Generously brush with butter; sprinkle evenly with half the nut mixture. Top with second phyllo sheet; repeat process. Top with third phyllo sheet. Brush with butter; sprinkle with thyme.
Using a 2-inch heart-shaped cutter, cut out hearts; transfer to a parchment-lined baking sheet. Lay a sheet of parchment over hearts, and bake until lightly browned and crisp, 12 to 15 minutes.