Preheat the oven according to the package instructions for the filo cups. Put the filo cups on a baking sheet and bake until golden brown and crispy according to the package instructions. Let cool.
In a medium bowl, mix together the cream cheese, salmon, creme fraiche, capers, shallot, lemon zest and juice, 1 tablespoon of the dill and 1 tablespoon of the chives. Transfer the mixture to a ziptop bag. Cut an approximately 1-inch opening in the corner of the bag. Pipe the salmon mixture evenly among the filo cups, filling them to the top.
Mix together the remaining dill and chives, then sprinkle some of the herbs on top of each cup to garnish. Serve immediately.