What is the best way to save a scene and load it later?

I have a script that saves the scene data to a file and uses AES 256 bit encryption to write the string to the file. It can then load the data to the point where it was saved. Unfortunately it only captures player location and a few other basic variables like health etc... Now what's the standard procedure for recording that snapshot of all of the variables and objects instantiated in the whole scene? I could have any number of prefabs loaded into a given scene so what's the correct way to record where those objects are and what their status is to save it until the next time the game is launched? I have a few strategies in mind but there must be a best practices procedure I could follow, any ideas?