Data from surface metrology, representing points in 3D space, are broadly relevant across numerous scientific and technological fields. These disciplines often employ a common set of operations for processing data. The most relevant examples are topographic maps from metrology instruments such as microscopes, profilometers, interferometers, but also any map of values over x,y coordinates, on which operations such as arithmetics, alignment, scaling, filtering, leveling and statistical analysis need to be performed in a repeatable and consistent manner. The typical Original Equipment Manufacturer (OEM) software, provided with metrology instruments, usually offer a large amount of functionalities and a quick way to analyze data and generate reports. However, this simplicity of use often comes with a limitation in flexibility. This is especially important in a research context, where custom analysis can be required, or when data from different instruments, each one with its own software, formats and operational parameters, need to be integrated. pyXsurf (documentation at https://pyxsurf.readthedocs.io) is an open-source flexible library for the realization of complex surface analysis, written in Python. The features of Python allow an easy integration with the many highly specific analysis and visualization tools available, and the possibility of integration in several flavors of interfaces, from GUI, to notebooks, to command line or scripting. The self-documenting capabilities of Python also enhance maintainability and allow a soft learning curve. We will give an overview of this package and present some usage examples taken from real-life research, mainly on metrology of astronomical X-ray mirrors. By fostering collaboration and contribution to the pyXsurf project, the research community can collectively enhance and refine this invaluable tool, promoting innovation and advancement in surface metrology analysis.