We report that dewetting of a thin polymer bilayer consisting of a stacked polystyrene (PS) film on top of a topographically patterned poly(methyl methacrylate) (PMMA) bottom layer on a nonwettable substrate results in a myriad of partially or fully ordered patterns. The local thicknesses of the thinnest parts of both the layers, that is, the residual layer thickness of the PMMA film after patterning (h R-PMMA ) and the local thickness of the PS film over the PMMA stripes (h T-PS ), collectively influence the evolution pathway and the extent of the ordering of the final dewetted features. In case both h R-PMMA and h T-PS are very low (≤9 nm), the films undergo near-simultaneous rupture over their respective thinnest areas, resulting in a morphology consisting of an array of ordered PS droplets surrounded by a holey PMMA matrix. In contrast, slightly thicker h T-PS (≈12 nm) leads to sequential rupture of the PMMA and the PS films over the substrate grooves, resulting in an array of core (PMMA)−shell (PS) threads. While the top layer flattens out along with the suppression of instability with a further increase in h T-PS (≈22 nm), the bottom PMMA layer still undergoes submerged directed dewetting. On the other hand, a slight increase in h R-PMMA ≥ 13 nm suppresses pattern-directed rupture of the bottom layer due to surface-tension-mediated flattening. Even on such a thicker bottom layer, an ordered array of aligned PS droplets exhibiting a Neumann configuration is obtained when h T-PS ≈ 9 nm. With a further increase in h T-PS , the ordering is completely lost in both layers. The nonwettability of the substrate hinders late-stage lateral coarsening of the dewetting features, facilitating the formation of ordered meso patterns by dewetting of a thin polymer bilayer with a topographically patterned interface. Finally, we also explore how various parameters such as the height of the PMMA stripes (h S-PMMA ), periodicity of the patterns (λ S ), and viscosity of the two layers influence the final dewetted features.