Most fingerprint recognition systems use Level 1 characteristics (ridge flow, orientation, and frequency) and Level 2 features (minutiae points) to recognize individuals. Level 3 features (sweat pores, incipient ridges and ultra-thin characteristics of the ridges) are less frequently adopted because they can be extracted only from high resolution images, but they have the potential of improving all the steps of the biometric recognition process. In particular, sweat pores can be used for quality assessment, liveness detection, biometric matching in live applications, and matching of partial latent fingerprints in forensic applications. Currently, each type of fingerprint acquisition technique (touch-based, touchless, or latent) requires a different algorithm for pore extraction. In this paper, we propose the first method in the literature able to extract the coordinates of the pores from touch-based, touchless, and latent fingerprint images. Our method uses specifically designed and trained Convolutional Neural Networks (CNN) to estimate and refine the centroid of each pore. Results show that our method is feasible and achieved satisfactory accuracy for all the types of evaluated images, with a better performance with respect to the compared state-of-the-art methods.