Fingerprint recognition has emerged as one of the most reliable biometric authentication methods, owing to its uniqueness and permanence. However, the security and confidentiality of the user’s data are key considerations in modern biometric systems. In this study, we describe an intelligent computational technique for automatically validating fingerprints for identification and verification purposes. The feature vector is created by fusing Gabor filtering features with deep learning techniques like the faster region-based convolutional neural network (Faster R-CNN). This study uses linear and decision-based median filtering (DBMF) techniques to minimize visual impulse noise. Faster-R-CNN with DBMF was applied to the feature vectors to reduce overfitting problems while improving classification precision and reliability. For fingerprint matching, the Euclidean distance between the associated Harris-SURF feature vectors of two feature points is used to measure feature-matching similarity between two fingerprint images. Furthermore, for fine-tuned matching an iterative technique known as RANSAC (Random Sample Consensus) is used. The experimental results collected from the public-domain fingerprint databases FVC-2002 DB1 and FVC-2000 DB1 show that the proposed design is viable and performs well with an accuracy of 99.43%, MSE value of 43.321%, and an execution time of 3.102 ms which was more exact than existing models.