Suffolk police homicide detectives and officials from the New York City medical examiner's office were also on the scene.
At least two dozen agents were gathered outside an office complex occupied by several businesses.
Agents also blocked off a section of woods.
Six markers were planted in the ground from the sidewalk to the building.
Eyewitness News has learned that agents are looking for the remains ofa notorious mob hit-man who has been missing since 1999.
William Cutolo, also known as Wild Bill, was a Brooklyn-born member of the Colombo crime family.
FBI agents arrived on the scene early Wednesday morning. They were expected to resume their search on Thursday morning.
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