With the rapid progress of network construction and informationization, security problems caused by widespread networking transactions have raised more and more concerns. In the network circumstance, one should verify the users’ identity before supplying the information service. Today, traditional identification methods based on the token and password cannot satisfy the security and privacy requirement. As a fast and exact identification method, biometrics has been widely used, which is the biggest application is the Automated Fingerprint Identification System (AFIS). Since there are no encryption methods being used in the traditional AFIS, the coordinates and the directions are stored as raw data in the template. The security and privacy of users’ identification is under threat. Traditional fingerprint template encryption is based on the Key Release method, which means overlapping the key and the fingerprint features, without any complex operation on them. Since the traditional key system has the disadvantage such as discommodiousness and forgetfulness. The security of whole key system is based on the password. The password can easily be cracked, and thus can affect the system security. We can bind the fingerprint feature with the key in a special way, and won’t be troubled by the storage and the management of secret keys. The secret key can protect the fingerprint template by itself, which makes the attacker difficult to get either the key, or the encrypted fingerprint template. This dissertation mainly concerns the research on template protection of AFIS. Firstly, we protect the fingerprint features in the template by key binding method. Secondly, we design a Fingerprint Fuzzy Vault scheme, and construct the algorithm platform of fingerprint template encryption. Finally, we propose an alignment algorithm in the encryption field. The main work of this dissertation is as follows: 1) We propose a Fingerprint Fuzzy Vault scheme based on the local structure of minutiae. The scheme binds the secret key with fingerprint features, which can give an efficient protection for the fingerprint template and the key. The scheme uses a minutiae filtering method based on the local image quality and the ridge structure, and improves the accuracy of encryption algorithm. It also takes the SHA-1 secure hash algorithm to protect and check the secret key, which makes the system more secure. 2) We also propose a fingerprint template encryption algorithm platform with extensible functions. Because of the open frame used in the algorithm platform, the core algorithms, such as the feature extraction algorithm and the polynomial reconstruction algorithm, can be replaced by more efficient algorithms. 3) We propose a fingerprint alignment algorithm based on topo-structure around the core point. The algorithm uses the topo-structure around the core point as Helper Data in the alignment in the encryption field.