It could mean nothing, or it could mean something. If the two of you are heading in the direction of no longer being 'ex's', maybe he is hinting he'd like to be more serious.

It could mean 'special' as in he values your friendship, and holds no grudges. Maybe he is saying you are 'special' as in, as a friend, and nothing more.

It may also simply be an endearment, you are special, so is his dog, his football team, his hockey stick.

Unless you ask him what he means by 'special', or wait for more clues, I wouldn't put too much stock into it.

Perhaps you are in a special kind of way.
Are you hoping it means he wants to be your boyfriend again?

Thanks but he has a girlfriend already

Well maybe you are special to him in a friendly way.