I am assuming this is a manual transmission. If it is an automatic transmission you need to remove the inspection cover on the bottom and unbolt the torque converter.
If it is indeed a manual, wiggle and pull. It was a pain in the butt to remove mine with it still in the bay, and I had to remove the crank pulley to have enough room to pull the engine over enough. If you don't remove it and your lifting it out from the top, you will catch on the body. After you get it separating you must make sure your free of the transmission shaft.