He recently went under the knife to cure the problem and should be ready for the first day of pre-season training next month.
By then Latics are expected to have signed another keeper to act as cover for Filan, and were yesterday linked with former player Carroll in the national media.
But manager Paul Jewell has knocked that rumour on the head and won't be going after the Northern Ireland international who has just been released by Manchester United. He said: "Roy is a top class goalkeeper but it is not in our plans to bring him back to Wigan.
"If he has turned down £20,000 a week at United it's hardly likely that he is going to come here."
One of Jewell's first tasks when he became Latics manager four years ago was to oversee Carroll's move to Old Trafford – the £3m transfer having been negotiated before he got the job.
It's likely Filan will again be first choice next season after signing a new two-year contract towards the end of last term. But Jewell wants a new keeper to act as cover and provide competition, with Rotherham's Mike Pollitt a possibility.
He's also been linked with Hartlepool's Greek keeper Dimi Konstantopoulos, although there doesn't look to be too much mileage in that one.
Turning to Filan's recent operation, Jewell said: "John played for three or four months of last season with a hernia. It's testament to him that he battled on with the injury and continued to maintain his usual high standards.
"He's had the operation now, he'll do his rehabilitation work through the summer and he should be able to take his place with the rest of the squad on the first day of pre-season training."
Latics' other two walking wounded, Jason Roberts and Nathan Ellington, are also making good recoveries from injury.
Roberts fractured his fibula during the final game of the season against Reading, while Ellington had an operation to repair a tear in his shoulder.
Jewell said: "Jason's last X-ray showed the fracture was healing well, and while any injury is a concern, it's not as if he's having to wear a plaster cast.
"He's resting the leg and will have another X-ray in the next few days to get an update.
"The Duke has a little while longer wearing a sling and after that can start getting the shoulder moving again.
"He might not be quite ready to start pre-season training with the rest but I don't think there's a doubt about him starting the season."
Meanwhile, season tickets will go on sale to existing holders on Monday, June 27, and on general sale a fortnight later.