At paleontological excavations, the use of digital surveying tools is becoming more frequent to measure the geographical location of specimens. This technology filtrates into the discipline of paleontology from archaeology, where the mapping methodology is quite similar, and the GIS as a standard tool for analysis is more widespread. The result of such a survey is a geodatabase, which forms the basis of subsequent analyses. The workflow is represented as the: 1) surveying, 2) database building, and 3) spatial analysis creating maps or 3D models. The presented methodological paper describes the details of the workflow, explaining the best practices and highlighting those issues which are necessary to be targeted even on the field. The methods tackle the optimal database structure, the spatial querying, which is managed from simple data table formats, and the 3D modelling. Explanations for these topics are given throughout specific programs; however, the tasks are also described generally enabling the reader to apply the described method to other programs. The data structure is explained through Excel worksheets, and for the analysis, an Excel-based macro script was developed, which is published as a supplementary material of this paper. Complex spatial analyses and visualization were done with Jewel Suite, a geological 3D modelling application. Demonstrating the workflow, three types of taphonomical inquiries are discussed using the surveyed materials of the Santonian dinosaur bed at the Iharkút site (Hungary). This technique is easily applied and becomes an important tool to obtain more precise taxonomical, taphonomical, and paleoecological interpretations in fossil excavations.