A lot of meteorites would be necessary for this to happen. Of course depending on how big and widespread the evidence would be. Some "well-directed" hits, and our footprints and scientific things would be gone. If they had a bigger base, they probably dug a lot of underground tunnels which are a lot more resistand (one of the reasons to build them to begin with).

The BBC actually made a documentary, showing what would happen, if the human race would suddenly vanish from earth: http://www.history.com/shows/life-after-people

There's a short summary on youtube: https://www.youtube.com/watch?v=Rh-lqtxZisA&feature=play...

[EDIT: The movie linked above talks about craters on the moon which are "billions of years" old.]

[Dinosaurs on the moon. What a crazy tought. But certainly interesting ;)]