Preheat your oven to 400°F / 200°C.
In a food processor, combine the Yogurt Cheese, cilantro, chipotle peppers, shallots, salt, and pepper.
Blend until the mixture is completely smooth and creamy.
Transfer the filling to a pastry bag, a food-grade squeeze bottle, or a resealable plastic bag (see tip below).
Prepare the peppers by using a small, sharp knife to make a slit crosswise at the top to create a hinged lid, keeping the stem intact. Gently open the pepper and remove any seeds.
Carefully pipe or spoon the yogurt cheese mixture into each prepared pepper until full.
Arrange the stuffed peppers close together on a baking sheet.
Bake for about 15 minutes, or until the filling is heated through and the peppers are tender but still have a slight crispness.
Serve immediately while warm.