Three-dimensional Direct Numerical Simulations combined with Particle Image Velocimetry experiments have been performed on a hemisphere-cylinder at Reynolds number 1000 and angle of attack 20°. At these flow conditions, a pair of vortices, so-called "horn" vortices, are found to be associated with flow separation. In order to understand the highly complex phenomena associated with this fully threedimensional massively separated flow, different structural analysis techniques have been employed: Proper Orthogonal and Dynamic Mode Decompositions, POD and DMD, respectively, as well as criticalpoint theory. A single dominant frequency associated with the von Karman vortex shedding has been identified in both the experimental and the numerical results. POD and DMD modes associated with this frequency were recovered in the analysis. Flow separation was also found to be intrinsically linked to the observed modes. On the other hand, critical-point theory has been applied in order to highlight possible links of the topology patterns over the surface of the body with the computed modes. Critical points and separation lines on the body surface show in detail the presence of different flow patterns in the base flow: a three-dimensional separation bubble and two pairs of unsteady vortices systems, the horn vortices, mentioned before, and the so-called "leeward" vortices. The horn vortices emerge perpendicularly from the body surface at the separation region. On the other hand, the leeward vortices are originated downstream of the separation bubble, as a result of the boundary layer separation. The frequencies associated with these vortical structures have been quantified.