Among the various multi-modal biometric approaches, multi-instance biometric appears to be understudied despite it inherits the merits of multimodal biometrics system. Multi-instance biometrics is useful when the signal quality is too low for robust verification. As compared to other multi-modal approach, multi-instance fusion reduces the need of multiple acquisitions using different sensors and thus lessen both transaction time and sensor cost. In this work, we propose a reliable two-stage multi-instance finger vein recognition system based on minutiae matching method by integrating a unified minutia alignment and pruning approach using Genetic algorithm and the k-modified Hausdorff distance (k-MHD) measurement. The proposed method is evaluated by using the SDUMLA-HMT Finger Vein database. Experiments show the proposed method is able to attain promising recognition rate compared to its single biometrics counterpart. The best result is achieved by applying the k-nearest neighbor measurement alongside, where the recognition rate can be up to 99.7% when MHD is used for matching.