The actor, who plays the android David in the Alien prequel, revealed that Scott is a big fan of improvisation in spite of being very "precise".
"He's just so precise and fun and mischievous and just full of interesting and quirky ideas for the character," Fassbender told the Los Angeles Times.
"They come to you in passing, but then he lets you run with it, and there's a lot of freedom there," he added.
Meanwhile, Scott spoke about the connection to Alien once again, insisting that Prometheus is its own story.
"This takes place in the same universe as Alien but it stands on its own as a story," he said.
"There's moments where you see connections if you're looking for them, but the story is not leaning on what came before. There are strands of Alien DNA in there, if you will," Scott finished.
Prometheus is scheduled for release on June 1 in the UK and June 8 in the US.