The applicability of computational analysis to paleontological images ranges from the study of the animals, plants and evolution of microorganisms to the simulation of the habitat of living beings of a given epoch. It also can be applied in several niches, such as oil exploration, where there are several factors to be analyzed in order to minimize the expenses related to the oil extraction process. One factor is the characterization of the environment to be explored. This analysis can occur in several ways: use of probes, extraction of samples for petrophysical components evaluation, the correlation with logs of other drilling wells and so on. In the samples extraction part the Computed Tomography (CT) is of importance because it preserves the sample and makes it available for several analyzes. Based on 3D images generated by CT, several analyzes and simulations can be performed and processes, currently performed manually and exhaustively, can be automated. In this work we propose and validate a method for fully automated microfossil identification and extraction. A pipeline is proposed that begins in the scanning process and ends in an identification process. For the identification a Deep Learning approach was developed, which resulted in a high rate of correct microfossil identification (98% of Intersection Over Union). The validation was performed both through an automated quantitative analysis based upon ground truths generated by specialists in the micropaleontology field and visual inspection by these specialists. We also present the first fully annotated MicroCT-acquired publicly available microfossils dataset. Introduction 1The applicability of computational image analysis to paleontological data encompasses 2 the possibility of identifying, reconstructing and visualizing microfossils in rock samples 3 not recovered by traditional extraction methodologies. It can also allow the taxonomic 4 1/16 microfossil identification even before the physical extraction from the rock sample. In 5 addition, it is also pertinent to verify the microfossil position in a given sedimentary 6 stratum, which can help in taxonomic inference, whereas detailed positional information 7 is lost in the traditional preparation method [8]. Computational analysis of samples can 8 be applied in several niches, e.g. oil exploration, habitat reconstruction and geology and 9 paleontology research. 10