Place phyllo cups on a baking sheet and bake for 5 minutes at 375. 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 plastic bag or pastry bag. Pipe the salmon mixture evenly among the 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.