They're interchangable, just as you thought.
CE, according to Webster, stands for Christian Era as well as Common Era, but Common Era is is the prefered usage in academia.
The obvious question is if the two designations are interchangable why change AD to CE?
There are different answers to that question depending upon whom you talk to. My own thoughts on the subject is the obvious denial of Christianity by a segment of academia. Common Era sound less religious than Anno Domini which translates into Year of Our Lord. After one or two generations of students who have been taught to use Common Era it will become standard usage and AD will be forgotten.
The irony is that some Christian churches also use Common Era instead of AD. I suppose those churches want to tone down the religious aspect of church services in favor of a more sensitive, secular, approach to religion.