Duffy served as an Assistant United States Attorney (1958–1959) and assistant chief of the Criminal Division (1959–1961) at the office of the United States Attorney for the Southern District of New York before going into private practice as an associate with the New York City firm Whitman, Ransom & Coulson (1961–1966).

[3] His tenure as Regional Administrator of the United States Securities and Exchange Commission was in a time of turmoil in Wall Street.

[6] In 1973, as a new member of the Southern District, Duffy was assigned one of the most complicated and difficult organized crime narcotics cases tried in Manhattan federal court, United States v.

[7] Carmine Tramunti and thirty others were charged with conspiracy to violate the federal narcotics laws in connection with many sales of heroin.

[10] In 1985, Duffy began a complicated multi-defendant trial involving the then-alleged leader and other members of the Gambino organized crime family.

"[11] Other defense lawyers have applauded the Judge's fair handling of the case and after the trial, the New York Post ran a headline calling him the "Avenger.

"[citation needed] Duffy presided over the trial of Ramzi Yousef, the mastermind of the Bojinka plot (the Manila Bombing Conspiracy), to hijack planes bound for the west coast of the United States and fly them into the Pacific Ocean on a coordinated schedule.

In the words of the Second Circuit, "Judge Duffy carefully, impartially, and commendably conducted the two lengthy and extraordinarily complex trials from which these appeals were taken.

"[15] Duffy ruled on post-trial motions of the defendant Wadih El-Hage (bin Laden's personal secretary) who had been convicted of conspiracy to kill Americans.

In an opinion spanning 54 pages of the Federal Supplement, Judge Duffy denied a motion for a new trial, after an evidentiary hearing.

"[19][20] Others, however, note that "during his twenty years as a member of the federal judiciary, Judge Duffy has impressed litigants, lawyers, jurors, and his colleagues as a jurist of rare legal acumen who gets right to the core of a case, a human being of unusual common sense, humor and humility.

[1] Because of his work in presiding over terrorism cases, Duffy was under security protection by the United States Marshal Service for ten years.