Slice the very top of the pepper off lengthwise, exposing the seed pod but keeping the stem intact. Reserve the sliced-off part of the pepper and dice them into small pieces. For the pepper itself, gently remove the seeds and excess white pith where the stem attaches and to create almost a boat-like vessel for the stuffing.
Once the peppers are cleaned, put them on a baking sheet and bake in the preheated oven for 15 minutes. Remove them from the oven and let them cool before stuffing.
STUFF AND COOK THE PEPPERS
While the empty peppers are baking, toast the pine nuts in a dry pan on medium heat for about 3-4 minutes. Combine the pine nuts with the muenster cheese and small-diced, raw excess pepper that you removed and stuff the par-cooked peppers with the mixture.
Put your now-stuffed peppers on the baking sheet and return to the oven for 5 minutes, then remove.
Turn your oven to broil and wait a few minutes for it to heat up. Place stuffed peppers in the oven on the center rack for about 2-3 more minutes or until the cheese is completely melted.
Once the peppers are done, remove from the oven, sprinkle the smoked paprika and thyme leaves on the peppers and serve!