A long-wave nonlinear analysis of the defect induced instabilities engendered by van der Waals forces in thin (< 100 nm) viscous bilayers is presented. The major focus of this study is on generation of periodic patterns and its miniaturization by exploiting the self-organized instabilities of thin bilayers; on topographically patterned substrates. A large variety of self-organized interfacial patterns such as periodic arrays of open and closed micro/nanochannels, isolated and encapsulated micro/nanodroplets, and membranes with ordered pores are obtained on different types of prepatterned substrates. In addition, we show that a bilayer can also be a suitable tool for (i) pattern transfer involving replication of the morphology of the lower layer interface to the free surface of the upper layer and (ii) generation of a mold by the upper layer material filling the periodic interstitial spaces formed by dewetting of the lower layer. Simulations suggest a profound influence of the substrate pattern directed lateral confinement, which governs the length scale of the dewetted structure when the substrate pattern periodicity is well below the spinodal length scale of the unstable bilayer. The influence of the initial configuration of the interfaces on the dewetting pathway and the dewetted structures are also shown.