1.You have stated "I have applied for fresh passport ". Do you mean that you have applied for a passport?
2.You have also stated "after I renewed my Birth Certificate I corrected it and changed my fathers name to "Rajan Vayalil Nair" (the correct one) at my local municipality sub registrar office". Why did you renew your birth certificates? Birth Certificates are not to be renewed at all. Did you mean than you have corrected the mistake made in your birth certificate? If yes, after how many years of issuing the original birth certificate, you had corrected it?
3. If you have corrected your birth father's name in your birth certificate, did you receive any fresh birth certificate?
4. The above information are required to advise properly,
5. However, passport office is very sensitive about the identification of the applicant which is established through those basic documents like birth certificate, school leaving certificate etc.,
5. You can file a declaratory suit before the court praying for an order declaring that your father's name is "Rajan Vayalil Nair" and directing the passport authority to recod it accordingly while issuing you the passport,
6. Alternatively your father can obtain a passport copy of which you can submit as desired by the passport authority.