The three accused are Mr Duffy, 49 of Forest Glade, Henry Fitzsimons, 48, of no fixed address and Alex McCrory, 55, of Sliabh Dubh View in Belfast.
All three are accused of directing terrorism, preparing terrorist acts and being in a banned organisation - the IRA.
They were released on bail.
Both Mr Fitzsimons and Mr McCrory deny attempting to murder members of the PSNI.
Those charges relate to a gun attack on a police convoy on north Belfast's Crumlin Road on 5 December, 2013.
They also deny possessing the two AK47 assault rifles and ammunition used in the attack.
A judge was told there would be a number of applications made to the court ahead of the trial.
These include reports linked to the covert surveillance of an alleged meeting between the three men in Lurgan Park the day after the attack on the police and regarding Mr Duffy alone, from secret recordings made in Mallorca.
Belfast Crown Court was told the non-jury trial is to start later this year and is expected to last between six to eight weeks.
Three men, including Lurgan republican Colin Duffy, have denied a range of terrorist related offences connected to a gun attack on police.