The building, located on North Greensboro Street, was recently purchased by CVS from the local co-op grocery store, Weaver Street Market.
On Saturday masked protesters, some who identify as anarchists and are loosely linked to the Occupy Chapel Hill movement, took over the building in an attempt to convert it into a community center.
Mayor Mark Chilton met with the protesters and personally asked them to leave before having the police step in and threaten arrest.
Chilton posted on his Facebook that he was "occupying the occupation."
Several members of the Carrboro Board of Aldermen were also present.
Eventually the protesters did leave the building but not quietly.
No arrests were made, and no injuries were reported.
After the building was vandalized during the occupation on Saturday, police remained on guard at the location overnight and throughout Sunday.
Some of the protesters involved in the Carrboro occupation were also present during the Chapel Hill occupation of the Yates building on Franklin Street.
Last November, Chapel Hill occupiers were met with heavily armed police.
That incident saw seven people arrested and two reporters detained.
A recent report released by Chapel Hill's town manager said the police were justified in their actions because they believed a group of anarchists were in the building, and it was believed they could be violent.
For months, many Carrboro residents have fought against efforts to allow CVS to build a store on the property.
Resident Jeff Herrick, whose wife is Michelle Johnson, a recently elected member of the Carrboro Board of Aldermen, said he does not agree with the protesters' methods.
"You can talk to the town planning board and figure what is the process CVS has to go through," said Herrick. "It's very boring, and it's not as exciting as taking over a building. But that's the way it works in Carrboro."
A public meeting at the Carrboro Town Hall is scheduled for Wednesday evening to help decide the fate of the property.