Mike, I'm not sure if by "it" you mean the cement bd. alone or the board and mortar bed. I think you'll want to take it in steps. Try to remove the CBUs with as little damage to the mortar bed as possible, next assess the shape of the motar bed. If it's in good shape, and your concern is to bring the flooring back up to the height it was with the CBUs, I would consider a self-leveling compound. If the mortar bed is toast, it should come out. If it is your intention to install new tile, the best thing at this point might be to just have the mortar bed replaced (a bit thicker maybe to get the height you want). If you're going to install some other flooring, building up a new floor with a plywood sub-floor is fine.