We investigated the influence of substrate confinement on the capillary breakup of parallel nonaxisymmetric polymer stripes suspended on top of, or confined between, another immiscible polymer pattern. When the residual layer thickness of the pattern was reasonably large, the PS (or PMMA) stripes confined within PMMA (or PS) trenches broke up, either nucleated, out-of-phase, or without clear phase correlation depending on the geometry and viscosity ratio between the two polymers. In stark contrast, for the two extreme cases of viscosity ratios we studied, in-phase breakup of confined polymer stripes was always observed when the alternating PS/PMMA stripes were formed, that is, without residual layer, regardless of the specific geometry.