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Boundary-layer flow separation is a common flow feature in many engineering applications. The consequences of flow separation in turbomachinery can be disastrous in terms of performance, stability and noise. In this context, flow separation is particularly difficult to understand because of its three-dimensional and confined aspects. Analyzing the skin friction lines is one key point to understanding and controlling this phenomenon. In the case of separation, the flow at the wall agglutinates around a manifold while the fluid from the boundary layer is ejected toward the flow away from the wall. The analysis of a three-dimensional separation zone based on topology is well addressed for a simple geometry. This paper aims at providing simple rules and methods, with a clear vocabulary based on mathematical background, to conduct a similar analysis with complex turbomachinery geometry (to understand a surface with a high genus). Such an analysis relies on physical principles that help in understanding the mechanisms of flow separation on complex geometries. This paper includes numerous typical turbomachinery surfaces: the stator row, vaneless diffuser, vaned diffuser, axial rotor and shrouded and unshrouded centrifugal impeller. Thanks to surface homeomorphisms, the generic examples presented can easily be converted into realistic shapes. Furthermore, classical turbomachinery problems are also addressed, such as periodicity or rotor clearance. In the last section, the proposed methodology is conducted on a radial diffuser of an industrial compressor. The flow at the wall is extracted from LES computations. This study presents the different closed separation zones in a high-efficiency operating condition. [ABSTRACT FROM AUTHOR]