Did you at some point run the program "Mirage"? If so (since that is the only program I know that turns the dock transparent and works great in 2D) then you need to check out how to undo it from that program. It is simple to undo, but I just don't remember at the moment how you do that- I think you just rerun it and tell it to restore the original dock, but I'm old and probably just imagined that!
On the other hand if you didn't run Mirage at some point all bets are off- and you can just use one of the free SuperDocker type programs to install a new dock of your choice which will take the place of the transparent dock.
