Copley Square is not on the Freedom Trail, but is not too far from Boston Common and is located in the Back Bay neighborhood. We saw it on the Duck Tour and returned on Monday morning before we flew home. The main three things to see are the Old South Church, Trinity Church and Boston Public Library.
The two churches both are beautiful on the outside and inside -- if you like architecture in the least, these are worth a visit. To visit Old South Church is free -- Trinity is $6 per person for either a self-guided or guided tour. Both are gorgeous.
We didn't have time to go inside Boston Public Library, but it is beautiful from the outside. According to our Duck Tour guide, it was the first truly free public library in the U.S. and holds millions and millions of titles.
Copley Square has a nice green space between the library and Trinity Church with a park-like feel and fountains on one side. Would be a nice place to rest your feet or read a book.