The Castle star revealed to DS that he expects to reunite with Whedon for a sequel to 2008 online serial Dr. Horrible's Sing-Along Blog.
"Do I think [a sequel is] ever going to happen? Yes, I do," he said. "I would lean more toward yes than no."
Fillion also discussed his time working on Whedon's 2002 sci-fi drama Firefly, in which he played Mal Reynolds.
"I think Firefly was popular because it was about people," he suggested. "You have this fantastic setting - it's the future, it's on a spaceship...
"But at the core of Firefly, it was about relationships and it was about people. It was about protecting those that are close to you and about just trying to do your best, in sometimes the worst of circumstances. It's been ten years and people still like that [show]."
> Firefly: Tube Talk Gold
Fillion will next collaborate with Whedon on a new version of Shakespeare's Much Ado About Nothing.
The 41-year-old actor revealed that he initially "tried to chicken out" of the project, as he struggled to get to grips with the play's language.
Fillion explained: "I called Joss and said, 'I don't know that I can do this - I don't want to hold everybody back...' and he just told me, 'Don't worry - this is gonna be fun'."
Nathan Fillion's Castle airs on Channel 5 in the UK.
> Nathan Fillion Castle Q&A: 'I would love six seasons' - video