The topology of the composite flow fields reconstructed by linear superposition of a two-dimensional boundary layer flow with an embedded laminar separation bubble and its leading three-dimensional global eigenmodes has been studied. According to critical point theory, the basic flow is structurally unstable; it is shown that in the presence of three-dimensional disturbances the degenerate basic flow topology is replaced by a fully three-dimensional pattern, regardless of the amplitude of the superposed linear perturbations. Attention has been focused on the leading stationary eigenmode of the laminar separation bubble discovered by Theofilis et al. (Phil. Trans. R. Soc. Lond. A, vol. 358, 2000, pp. 3229–3324); the composite flow fields have been fully characterized with respect to the generation and evolution of their critical points. The stationary global mode is shown to give rise to a three-dimensional flow field which is equivalent to the classical U-shaped separation, defined by Hornung & Perry (Z. Flugwiss. Weltraumforsch., vol. 8, 1984, pp. 77–87), and induces topologies on the surface streamlines that are resemblant to the characteristic stall cells observed experimentally.