Heat clarified butter over medium-high heat in a large pot or Dutch oven. Sear the beef on all sides for 10 minutes, then add the diced onion and cook for 10 minutes more.
Season with pepper and stir in the diced garlic. Deglaze the pot with roughly 1/4 of the red wine, scraping up the browned bits. Add the bay leaf and thyme.
Pour in the remaining red wine and meat broth. Bring to a simmer, cover, reduce heat to low, and braise for 3 hours, stirring occasionally and adding more wine every hour as needed to keep the meat mostly covered.
Remove the beef from the pot and let it rest for 5 minutes.
Pour the meat resting juices into the pot. Using an immersion blender or food processor, puree the sauce until smooth.
Stir in the creme fraiche cheese and season to taste.
Slice the beef and serve with the sauce on the side.