He said on Sky Sports: "You have to build the team around Bruno (Fernandes). He's quality and has got fight in him, and then I think all the other players get rid of them.
"I think you keep the young players, and you keep Bruno.
"I think it has to be a massive clear out. It has to be. It's not going to be in one year, but I think it's going to be in the next couple of years.
"I think he (Andre Onana) has had a shaky start but has got better and better over the year.
"For me, (Diogo) Dalot's done well, Maguire has had an in and out season.
"To compete in this league they need better players. Don't get me wrong these players are good players. But to compete with Man City, Liverpool and Arsenal, they need better players."
Rooney also spoke on former team-mate Marcus Rashford, "We all know Marcus has the capabilities to play at the top level, and we haven't seen it.
"I just wonder is it time for Marcus to go and play somewhere else. I think he has to ask himself that question. I want him to stay and break records at this club. He needs to work hard and get his head down."