User Authentication plays a crucial role in smart card based systems. Multi-application smart cards are easy to use as a single smart card supports more than one application. These cards are broadly divided into single identity cards and Multi-identity cards. In this paper we have tried to provide a secure Multi-identity Multi-application Smart Card Authentication Scheme. Security is provided to user’s data by using dynamic tokens as verifiers and nested cryptography. A new token is generated after every successful authentication for next iteration. Anonymity is also provided to data servers which provides security against availability attacks. An alternate approach to store data on servers is explored which further enhances the security of the underlying system.