It looks like the archaeologists are digging through ordinary earth but they are actually searching through an ancient rubbish dump that surrounds the houses. Archaeologists call this the midden.
After the really big stuff, like bits of bone, pottery and sea shells, have been found, the midden is riddled through a sieve to find smaller items like fish bones.
Next the midden is washed which helps find things like tiny plant seeds when they float to the top. All the things found are important clues about the people who lived here.
At Skara Brae, the archaeologists dug down through 4 metres of midden, all the way to the original ground level of the village. As they dug down they could see that there were 2 villages, not just one.
The village you can visit nowadays has been built on top of an older village that is buried deep down under the midden. After a while the village on top became surrounded by the midden.
There had also been earlier settlers in the area, even before Skara Brae was built.