Tomographic particle image velocimetry (TPIV) measurement with six high-resolution charge-coupled device (CCD) cameras is conducted to investigate flow structures over a finite circular cylinder with an aspect ratio of 2 (
). This short wall-mounted cylinder is fully immersed in a thick turbulent boundary layer (
). Focus is placed on the three-dimensional instantaneous vortex structures and their dynamic characteristics in the wake flow fields. Based on the present results, a refined topological model of the mean wake field behind the finite circular cylinder is proposed, where the spatial locations of the typical vortex structures and their interactions are described in more detail. Among the reported typical vortex structures (i.e. the horseshoe, tip, base, trailing and arch vortex), emphasis is laid on discussion of the tip and arch vortex. The instantaneous 3D M-shape arch vortex and an alternating large-scale streamwise vortex are first found in the present experiment, and their developments are also discussed. Therefore, it is suggested that the instantaneous finite-cylinder wake is dominated by the arch vortex system and the large-scale streamwise vortices. Moreover, in the instantaneous volumetric flow fields, both the antisymmetric and the symmetric wake behaviours are observed. With proper orthogonal decomposition (POD) analysis, the dynamic characteristics of the wake field are clarified. Different from the flow around an infinite cylinder without control, the third and fourth POD modes are characterized by low-frequency symmetric shedding. The low-frequency feature shown in the second mode pair is observed and associated with the occurrence of instantaneous symmetric 3D wake behaviour triggered by the low-aspect-ratio effect and the extension of the separated shear layer. The low frequency seems be attributed to the flapping phenomenon, i.e. oscillation of the recirculation in the backward-facing step flow. It is found that the flapping motion has a modulating effect on the occurrence of the antisymmetric shedding vortex and thus the large-scale streamwise vortex.