In this paper, a neural network structure based on self organizing feature maps (SOFM) is proposed for fingerprint classification. In order to be able to deal with fingerprint images having distorted regions, the SOFM learning and classification algorithms are modified. For this purpose, the concept of "certainty" is introduced and used in the modified algorithms. This fingerprint classifier together with a fingerprint identifier, constitute subsystems of an automated fingerprint identification system, named HALafis. Our results show that a network that is trained with a sufficiently large and representative set of samples can be used as an indexing mechanism for a fingerprint database, so that it does not need to be retrained for each fingerprint added to the database.