The fingerprint is a widely adopted biometric trait in forensic and civil applications. Fingerprint biometric systems have been investigated using contact prints and latent and contactless images which range from low to high resolution. While the imaging techniques are advancing with sensor variations, the input fingerprint images also vary. A general fingerprint recognition pipeline consists of a sensor module to acquire images, followed by feature representation, matching and decision modules. In the sensor module, the image quality of the biometric traits significantly affects the biometric system’s accuracy and performance. Imaging modality, such as contact and contactless, plays a key role in poor image quality, and therefore, paying attention to imaging modality is important to obtain better performance. Further, underlying physical principles and the working of the sensor can lead to their own forms of distortions during acquisition. There are certain challenges in each module of the fingerprint recognition pipeline, particularly sensors, image acquisition and feature representation. Present reviews in fingerprint systems only analyze the imaging techniques in fingerprint sensing that have existed for a decade. However, the latest emerging trends and recent advances in fingerprint sensing, image acquisition and their challenges have been left behind. Since the present reviews are either obsolete or restricted to a particular subset of the fingerprint systems, this work comprehensively analyzes the state of the art in the field of contact-based, contactless 2D and 3D fingerprint systems and their challenges in the aspects of sensors, image acquisition and interoperability. It outlines the open issues and challenges encountered in fingerprint systems, such as fingerprint performance, environmental factors, acceptability and interoperability, and alternate directions are proposed for a better fingerprint system.