I had a funny discussion with some friends about that during college. We were drinking and joking around and creating all sorts of stupid reasons for why aliens were conducting anal probes, but one guy had serious and interesting theory:
Human feces contain all of the body’s solid wastes. The solid waste is obviously composed of digested food but also dead cells of every type (blood, brain, heart, etc.), antibodies, antibiotics, viruses, bone marrow and everything else inside of us. If you want to gather a sample of everything inside the human body, the least invasive and quickest way to do that would be to extract a stool sample. And assuming they are indeed several hundred or several thousand years advanced in technology, it wouldn’t pose a problem for them to seperate the biological material from the feces and then study, catalogue or duplicate it for whatever purpose they want.
I remember that because we were having such a great time with lots of laughs and then he said that and everybody just got silent. It was a total buzz kill.
Any civilization advanced enough for star travel does not need to go up our butts to scan us completely, utterly and to the very core of everything that makes up all of our matter, and all matter and energy in the universe when they are done glancing our way.
If anything it is for their vacation photos where they show their friends and laugh about how this ones eyes bulged out when we rammed in the probe kind of thing.
LOL.