Saturday's 0-0 draw with Reading means that both clubs will be playing Championship football next season, yet Fernandes has remained upbeat about the future of the Hoops.
"Chris would be a tower in the Championship and it would be fantastic to build a team around him," Fernandes told Sky Sports News.
"We're under no pressure now to just keep players so if Chris wants to stay with us, if he believes in what the club can do, then I'd love him to be one of the pivotal points of the Championship side.
"But if he doesn't feel that this is right for him then I don't want to force him to stay. We want players who are excited by walking down that tunnel and going to play for us."
Samba arrived at Loftus Road in January for a fee reported to be in the region of £12.5m.