First make sure the refund request is accurate, then, i would usually write up a refund request with documentation attached for the doctor to approve. If he approves it then send the check to the refund address. You could let them recoup it depending on the payor. I mean if its not bcbs, UHC, etc (guru payers) then you just as well mail the check.
Often times this will depend on the insurance carrier. Most often you will issue a check from the providers office with the attached documentation (EOB, etc) providing the carrier with the return of the overpayment. Some carriers prefer to retract (or take-back) the monies on a future EOB.
Check your contracts, often time this is specified as part of the contract between you and the carrier. Or the carrier may have a special form or address to be used when monies are returned. If you are unsure talk to your regional representative from the carrier/insurance for direction as well.