A meeting on Monday morning with Harry Redknapp resulted in the Rangers boss committing his future to the club - and now the pair have begun to plan for life after relegation.
"We've been through who Harry wants to keep and who he is happy to let go," Fernandes told the club website. "The transfer policy is in place now for next season and beyond.
"There are some that will want to stay, others that might want to move on.
"I am a positive person, so people will say I'm not being realistic, but if you go through player by player, we'll sort it out. It's not insurmountable."
Much has been made of the challenge the club faces in trying to sell players who are on good contracts at Loftus Road, but Fernandes insisted it was not of great concern to him and Redknapp.
"Every football club in England has players that the manager would rather was not there - that's a function of the game," he said. "I don't think we're going to be in a bad position from that. We'll come out of it okay."
Fernandes believes the development of the squad since his arrival two years ago means the club are now in a far stronger position when it comes to the transfer market.
"A lot of our investment has gone into building up the squad," he added. "Now we're in a position where we can trade. We weren't able to do that before - we were just buying, buying and buying.
"The policy was how long do we sign a player for and what kind of wages are we paying. That's all been cleared up now though.
"I think a lot has been made of us letting players from the Championship winning side leave the club, but if you go through all of those players who moved on that had contracts with us, none of them moved on to go and play in the Premier League.
"Some of them are playing in the bottom half of the Championship."
Fernandes oversaw an influx of big-name players within days of his arrival at the club in August 2011, and he confesses there were times when he queried some of the potential acquisitions.
"At the time when we arrived we were offered a lot of players, many on free transfers," he explained.
"We questioned a few of these and it wouldn't be fair for me to name names, but we weren't long in the business and we deferred to the footballing side of the business. At the end of the day, we went with what the footballing side said."