The Southern California locations where Agents of S.H.I.E.L.D." is filmed.

Episode 2 is set almost entirely in Llactapata, Peru, as the S.H.I.E.L.D. team flies there to
investigate the discovery of an O-8-4 (an object of unknown origin).

It won't surprise anyone to learn that they didn't really go all the way to Peru to film these scenes.

So, where in L.A. did they find the tropical vegetation and dirt roads they needed?

These scenes were shot at the South Coast Botanic Garden, an 87-acre public garden, at
26300 Crenshaw Blvd, on the Palos Verdes Peninsula,  in the South Bay area of Los Angeles.

The view of the pre-Incan temple itself was, of course, mostly CGI and green screen,
so don't expect to find that at the Garden. So was the initial scene of the cargo plane
flying past mountains into Peru. But otherwise, all of the shots of them driving on
dirt roads through the jungle, or battling soldiers, were shot in the garden.

The garden itself is a man-made creation. Amazingly, until 1961, the area had been a landfill.

The county (and local volunteers) did a marvelous job of converting what could have otherwise
been an eyesore into a lush, tropical Eden. Most of the garden isn't jungle-like, of course -
beyond the lake, they have rose gardens, white gazebos, grassy lawns, a children's garden
with nursery rhyme cottages, a cactus garden, a gift shop, flower shows, etc.

To find the garden, from Pacific Coast Highway in Torrance, just turn southwest up Crenshaw Blvd
and go less than a mile up the hill. The entrance to the garden will be on your left (southeast) side.

(Here's the garden's website.)

If you're familiar with the TV show "Dexter", then you've seen this garden before.
The lake at South Coast Botanic Garden was where they filmed the 2nd season
scenes where Dexter imprisoned Doakes in a cabin (before Lila blew it up).
The show used it again in the 4th season, for scenes of Dexter & Trinity in the woods.

Here is a Google StreetView of the entrance to the garden.