Saturday, March 1th 2003, 7:30AM

Using DNA profiles from the FBI, the city medical examiner's office has identified the remains of two Sept. 11 hijackers, officials said yesterday.

The remains had been kept with other unidentified and unclaimed body parts in Memorial Park at 30th St. and First Ave., behind the medical examiner's office.

The terrorists' remains have been removed, but what will be done with them is unclear, said Ellen Borakove, a spokeswoman for the medical examiner.

She said her office doesn't know which of the terrorists' remains were identified because the FBI profiles did not have names attached to them.

John Cartier, a member of the victims' advocacy group Give Your Voice, said he was relieved to hear the terrorists' remains had been separated from the others.

"I think they should be used as dirt in the road," said Cartier, whose brother, James, died in the World Trade Center attack.

Ten terrorists hijacked the two airplanes that crashed into the twin towers on Sept. 11, 2001.

Years of work

To identify remains of victims, the medical examiner's office asked family members to provide items such as toothbrushes from which DNA samples could be gathered.

In the case of the hijackers, authorities developed DNA profiles from items the men were believed to have handled or possessed, FBI spokesman Paul Bresson said.

The effort to identify remains is expected to continue for years.

Of the 2,792 people listed as missing, the remains of 1,468 have been identified.

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