Recently, a cryptographic construct, called fuzzy vault, has been proposed for crypto-biometric systems, and some implementations for fingerprint have been reported to protect the stored fingerprint template by hiding the fingerprint features. In this paper, we implement the fuzzy fingerprint vault, combining fingerprint verification and fuzzy vault scheme to protect fingerprint templates. To implement the fuzzy fingerprint vault as a complete system, we have to consider several practical issues such as automatic fingerprint alignment, verification accuracy, execution time, error correcting code, etc. In addition, to protect the fuzzy fingerprint vault from the correlation attack, we propose an approach to insert chaffs in a structured way such that distinguishing the fingerprint minutiae and the chaff points obtained from two applications is computationally hard. Based on the experimental results, we confirm that the proposed approach provides higher security than inserting chaffs randomly without a significant degradation of the verification accuracy, and our implementation can be used for real applications.