Nearly 10 years later, 9,041 pieces of human remains - mainly bone fragments, but also tissue that has been dehydrated for preservation - are still being sorted as the city's medical examiner searches for DNA.
Now, a dispute over what to do with those remains is simmering between some of the victims' families and the officials planning the National Sept 11 Memorial and Museum underneath where the twin towers stood.
The plan is to take the remains�seven storeys down, behind a wall in the new museum, with a quotation from Virgil about never forgetting created in letters made from World Trade Center steel. But the opponents are appalled by the idea of remains that could belong to their loved ones being turned into a lure for tourists, and want them kept in a separate above-ground memorial that would be treated like hallowed�ground.
'I personally feel I've been robbed of access to where my son's remains are potentially being buried,' said Ms Sally Regenhard, the mother of a firefighter who died on that day.
How to handle remains is one of the most delicate questions in commemorating the darkest chapters of human history. Over the past 20 years, museums across the US have grappled with how to repatriate Native American skeletons, scalps and bones to their tribal heirs, as prescribed by a 1990 federal law.
The United States Holocaust Memorial Museum in Washington decided against displaying human hair from Nazi death camps when some survivors felt it would be offensive.
In Oklahoma City, unidentified remains of the 168 victims of the 1995 bombing are buried under a grove of 168 trees about 4km from the museum chronicling the events.
In Shanksville, Pennsylvania, where Flight 93 crashed on Sept 11, 2001, only family members are allowed access to the crash site, which is assumed to contain some remains of the 40 passengers and crew members.
The plan at the World Trade Center is for the remains to be invisible and inaccessible to the public, with an adjoining room for victims' families to contemplate and grieve. Museum director Alice Greenwald said that because the museum would be at Ground Zero, it had a special place in history.
Ms Greenwald said that was what a 'majority of families have actually said over the years' that they wanted.
The dissenting families support a plan for placing the remains in something akin to the Tomb of the Unknowns, separate from the museum.
'When you go to the genocide museum in Phnom Penh, when you go to genocide museums all around Rwanda, there have been decisions in those places to present corpses, skulls, evidence of human remains. When you go to Auschwitz, the entire facility is made up of human remains,' she said.
'The only place one could repatriate those remains to is the World Trade Center site.'
NEW YORK TIMES
