Meaning: The farmer removed the dirt from the place where the animals live.
Choice of Words: A "farmer" is a person who works on a farm. "Cleaned" means to make something free from dirt or mess. A "pen" is an area where animals are kept. "Muddy" means covered in mud, which is a mixture of water and soil. So, "Farmer cleaned the muddy pen" means that the farmer removed the dirt and mud from the area where the animals are kept.