RIO BRANCO, Brazil — Edmar Araújo still remembers the awe.

As he cleared trees on his family’s land decades ago near Rio Branco, an outpost in the far western reaches of the Brazilian Amazon, a series of deep earthen avenues carved into the soil came into focus.

“These lines were too perfect not to have been made by man,” said Mr. Araújo, a 62-year-old cattleman. “The only explanation I had was that they must have been trenches for the war against the Bolivians.”

But these were no foxholes, at least not for any conflict waged here at the dawn of the 20th century. According to stunning archaeological discoveries here in recent years, the earthworks on Mr. Araújo’s land and hundreds like them nearby are much, much older — potentially upending the conventional understanding of the world’s largest tropical rain forest.

The deforestation that has stripped the Amazon since the 1970s has also exposed a long-hidden secret lurking underneath thick rain forest: flawlessly designed geometric shapes spanning hundreds of yards in diameter.