The all-glass facade of the new Apple flagship store on Boylston St. initially raised some concerns from the Back Bay Architectural Commission.

Two years after a city architectural commission raised questions about its design, an Apple store opened on Thursday across from Boston’s Prudential Center.

“Some folks doubted this day would ever happen,” said Mayor Thomas M. Menino, referring to the Back Bay Architectural Commission’s (BBAC) initial opposition to razing the Copy Cop building at 815 Boylston St. and replacing it with Apple’s 3-story glass showcase. “But with all of us working together we have this beautiful Apple store – the largest in America.”

The Menino administration hammered out an agreement between Apple and the BBAC that allowed demolition of the 100-year-old building in favor of one with a glass façade. The 21,350-square-foot store boasts three floors of retail space with a glass staircase. The first floor features computers, the second level offers iPods and third floor is devoted to technical support.

Apple’s megastore is a first for Boston. The California-based computer giant has eight stores in Massachusetts, including locations in Braintree, Burlington, Cambridge, Chestnut Hill and Peabody.