Latter is at the end. Being the second of two persons or things mentioned; near or nearer to the end. It has more to do with placement, so to speak. Location, real or figurative.
Between captain and major, the latter is the higher rank.
My favorite is the latter part of the book.
Later has more to do with time.
She arrived an hour later than expected.
Better plant your tomatoes later in the Spring than sooner; tomatoes don't do well in the cold.
They are similar, but not interchangeable. You can't say "I'd prefer the later" if asked if you would prefer coffee or tea. You can't say, "Plant them latter in the season."
You can say, in the latter part of Spring, as with the latter chapters of a book.
You can say, I'd like some coffee, but later, please.