How do i remove the Scion 1NZFE Engine?

You will need to start by draining the engine oil and coolant, disconnect the battery. Also, the instructions call for the removal of the engine with the transaxle which will come out from the bottom. Remove the CV axles and the car will need to be lifted. Here are the instructions on how to remove the engine and transaxle. Check out the images (below). Let us know if you need anything else.

Can i remove it by itself without the transmission? I have seen people remove the engine without the transmission on the same engine.

It might be possible; they don't give information for it though. Only what I gave you is what we have. If you run into issues doing the job, please upload images or short videos of the problem so I can help if needed.