The complex three-dimensional (3D) flows around a short cylinder on the wall, acted by a flow exiting from a fore angled hole (FAH) that penetrates the cylinder from the fore to the top end, were experimentally investigated. The 3D instantaneous velocity distributions were measured based on tomographic particle image velocimetry (Tomo-PIV). The 3D flow structures behind the FAH and no-hole cylinders are compared in terms of the measured 3D velocity and vorticity distributions, Q-criterion, and tip vortices. A 3D W-type arch vortex, which shows a larger peak or convexity on the horizontal part center than for the no-hole cylinder, is found around the FAH short cylinder. The exiting flow from the FAH increases the separation zone, and FAH height effectively controls the eddy structures. The instantaneous 3D velocity data obtained from Tomo-PIV are decomposed using 3D wavelet multiresolution analysis and proper orthogonal decomposition. With the FAH cylinder, the large-scale streamwise wake vortices are smaller than with the no-hole cylinder, and this exhibits more evident as increasing the FAH height. The time-mean 3D large-scale arch vortical structures, however, become stronger. Proper orthogonal decomposition indicates that the energetic flow structures of the FAH cylinders are stronger than those of the no-hole cylinder.