Pure cotton is microwave safe as long as you do not expose it for too long. As little as five minutes has a huge impact on the durability of the fiber. Cotton and other natural fibers are fine to go through quick microwave drying. Microwave heating or drying is not advisable for cotton batting. It does not affect the elongation of the fibers, but it affects the fiber’s strength. When you microwave any cotton fiber, it decreases its strength by 10 percent. This significant decrease happens only for five minutes of microwave exposure. If you want to clean and dry your cotton batting, pre-wash it before using it.