NASA put 16,000 square feet of shrink-wrap around the spacecraft while crews build a museum around it.
The shuttle is going to be the centerpiece exhibit at the Kennedy Space Center Visitor Complex.
NASA wants to make sure the orbiter isn't damaged by any dirt or debris during the construction.
Atlantis' mission in 2011 marked the end of the United States' shuttle program.
It completed 33 missions over its service.
The museum is expected to be open to the public by July.