Cohen plays a train station inspector trying to find orphan Hugo, who has been living at the station and maintaining its clocks. Hugo befriends a girl called Isabelle, whose adopted father Georges (Ben Kingsley) owns a toy shop at the station.
Scorsese recently described the process of making a 3D movie as "an enjoyable headache".
"Most people have stereoscopic vision so why belittle that element of our existence?" the Oscar-winning director said.
"Why not use it? Everything moves along and there's no major catastrophe. We're basically headed for holograms. You have to think that way."
Hugo is in US cinemas now and will open in the UK on December 2.
> Martin Scorsese's 3D Hugo to get Royal premiere
> Hugo: Watch the new trailer for Martin Scorsese's 3D film