The sifting of over 800 cubic yards of debris recovered from ground zero and underneath roads around the site began in April and ended Friday.
The greatest number of remains - 37 - were found from material underneath West Street, a highway on the west side of ground zero.
The new debris was uncovered as construction work made new parts of the site accessible.
The city began a renewed search for human remains in 2006. More than 1,800 remains have been found.
Some have been matched to previously unidentified 9/11 victims.
