I had to remove the ceramic tile from my entire bathroom floor because of water damage by the toilet. The water damaged area was repaired. I now want to lay new ceramic tile back down on the floor. The problem is the old cement board now has all the grooves that was used to secure the original tiles down. What can I do to smooth the floor without having to remove all of the cement board?

You can scrape as much of the old substrate off, apply a thin coat of floor leveler and then defile.