A free root can stand alone with nothing added to it.
Given that it is 'free,' it can exist alone and doesn't have to have either prefixes or suffixes added to it in order to exist as a word. A root is the smallest part of a word (when you take off prefixes and suffixes) that still has a meaning.
For example: unbelievable - here, the root is believe, the prefix is un- and the suffix is -able.