Assuming that whatever computer is processing your blueprint could accurately detect all of your poop and pee, then I don't see why it couldn't physically do that.

Heh, well, there might be a pressure problem... but yeah if it's accurate enough to put all of the walls of your intestines back where they were, why bother reconstructing that log inside there? But then... do you fill the empty space with vacuum? air? fluid? or do you try to reconstruct the intestine, not as it was, but in a relaxed/empty state?

Better question yet is if it's possible to tamper the blueprint, where would the limit be? Could it be used medically to essentially perform surgery on you (or rather your clone)? Could the teleporter service basically offer you a character creation screen to make yourself however you'd want to look or be?

If we can get rid of your waste, we can at least get rid of kidney stones too, right? And probably tumors and parasites, maybe even bacterial infections.