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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 …