Fingerprint recognition systems have been applied widely to adopt accurate and reliable biometric identification between individuals. Deep learning, especially Convolutional Neural Network (CNN) has made a tremendous success in the field of computer vision for pattern recognition. Several approaches have been applied to reconstruct fingerprint images. However, these algorithms encountered problems with various overlapping patterns and poor quality on the images. In this work, a convolutional neural network autoencoder has been used to reconstruct fingerprint images. An autoencoder is a technique, which is able to replicate data in the images. The advantage of convolutional neural networks makes it suitable for feature extraction. Four datasets of fingerprint images have been used to prove the robustness of the proposed architecture. The dataset of fingerprint images has been collected from various real resources. These datasets include a fingerprint verification competition (FVC2004) database, which has been distorted. The proposed approach has been assessed by calculating the cumulative match characteristics (CMC) between the reconstructed and the original features. We obtained promising results of identification rate from four datasets of fingerprints images (Dataset I, Dataset II, Dataset III, Dataset IV) with 98.1%, 97%, 95.9%, and 95.02% respectively by CNN autoencoder. The proposed architecture was tested and compared to the other state-of-the-art methods. The achieved experimental results show that the proposed solution is suitable for recreating a complex context of fingerprinting images.