Open pit mines seem to be a pretty good candidates for this. They're pretty much the opposite of a structure, but I can't imagine them looking "natural" even thousands of years from now. I can imagine one or two getting overgrown, but ones in desert areas like Utah could last until the next deep ice age.

Yeah I guess you can look at ancient craters from meteors or volcanos to see how it would look.

Can we? I'm not under the impression that those were ever terraced[1] like open-pit mines. But come to think of it, terracing itself qualifies as a megastructure[2]. Where the Long Now clock is an offbeat art project, rice paddies are crucial for nutrition for a great many people and they've already been around for at least 2 millenia. As times get lean, I can imagine pilfering the Long Now clock for parts; but those rice paddies will only gain importance.

[1] https://www.dreamstime.com/stock-photography-bingham-kenneco...

[2] https://en.wikipedia.org/wiki/Rice_Terraces_of_the_Philippin...

Terraced open pit mines and rice paddies require an enormous amount of maintenance. The terraces are not naturally stable. Rice paddies will quickly silt-up, then flood and collapse in heavy rain.

Open pit mines will fill with water. The sides will collapse. In the desert, they will fill with dust. Deserts often have flash-floods following thunderstorms. They might remain recognizable as hollows, but not much more.

The Bingham mine has had collapses in 2013 and 2021:

https://blogs.agu.org/landslideblog/2021/06/04/2021-bingham-...

https://blogs.agu.org/landslideblog/2013/04/30/analysing-the...

https://blogs.agu.org/landslideblog/2013/05/06/analysing-the...

There was a similar collapse recently at the Çöpler Mine in Turkey...

https://eos.org/thelandslideblog/copler-mine-1

https://eos.org/thelandslideblog/copler-mine-2

https://eos.org/thelandslideblog/copler-mine-3

https://www.youtube.com/watch?v=SUD0hQjueI0

https://www.youtube.com/watch?v=SCRTwnz3_oo

There's a good book, The World Without Us that goes into great detail on what would happen if humans disappeared.

Hoover dam? Svalbard seed vault?