Is there a prefix or a suffix in supernatural?

Yes, "super" would be the prefix in the Word "supernatural". If you look at the Word, it's basically two Words in one - super and natural. Natural is the base Word and super is the Word added to the beginning of it to emphasize or contribute to the original meaning. Something can be natural, but by adding the prefix "super" the meaning changes so that it is more than, or above and beyond natural.