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Your question is a bit confusing.
You choose the destination volume (the target), on a separate drive, of course, and Time Machine creates its own folder on that destination.
You might have Time Machine ignore everything on the source but a single folder.
You would not really be using Time Machine in a very efficient manner, however. You may be better with using some other backup solution, such as CCC or SuperDuper!, either of which can be set up with a lot of granularity, if that's what you prefer.