Prehistoric means before writing thusly pretty much anything older than 8000 BP qualifies. The first part of the question should be "was there civilization?", that depend on the definition of civilization if it means communities larger than 200 people perhaps, at the very edge of proven known fact is there are the remains of the temple at Göbekli Tepe which dates back between to 10000 & 12000 BP. The second part of it is "if these civilizations existed were they advanced" this too depends on what one considers advanced. The artwork of Göbekli Tepe is incredibly good as and could be considered a few thousand years more advanced compared to their neighbors, but it is stone work and wood carving. Metal working really doesn't show up anywhere until about 8000 BP. And those are the crucial two test items to find if you are looking for something more advanced than say the Greeks or the Romans, the first is identifiable advanced stonework and the second is items made of a metal substance that has not corroded into something unrecognizable. Pottery is nice but nearly everyone makes that even pre-12000 BP, and everybody can draw imaginary things. The best date to look for real advancement is 8000 BP, and the best place to look for that IMHO is the Danubian Basin with peoples like the Vinča, Kurgan, and Proto Indo Europeans.
As for pyramids, the reason to build in that shape is stability at height, building straight up without the necessary technologies becomes very unstable. If aliens were involved in pyramid building, for some reason they did not impart the knowledge of how to build a True Arch, the pyramids have False Arches (counter balanced blocks) in them. Besides Aliens don't visit here we are backwater planet with nothing interesting going on.
And as for Atlantis forget it. Plato wrote the about Atlantis and in his style of writing he wrote it as he heard it about 5x removed from the source, this was his way of saying it is a fictional place. 5x removed from the source is like saying "I'm telling the story (1), I heard it from you (2), You heard it from your cousin (3), he heard it from his grocer (4), who heard it from a vagrant (5). Plato puts this fictional civilization at around 12000 BP which would make it as old as Göbekli Tepe, however the description is incredibly detained the type of stone blocks used in its walls and there color, the number of concentric ring walls and the distances between walls, what Gods they worshipped (for some odd reason it's Poseidon even though he was not invented as early as 12000 BP) and then of course a highway system of canals with some kind of overpass system with locks. It was these fictional details which made people think the place was real, but for Plato they were just symbolic tools to create a fictional stories illusion of perfect order. First order of business when telling a fictional story suspend disbelief. So if you are looking for Atlantis and you think Plato was telling the truth those are the things that must be found, and that hasn't been found nor will it be. So like I said focus your attention on the Danubian Basin and you might find the earliest writing and civilizations.