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In this paper, we demonstrate an assisted self-assembly fabrication method for unidirectional patterns using pre-programmed shape memory polymer (SMP) as the substrate in an organic/inorganic bi-layer structure. By heating the hybrid structure above the SMP's shape recovery temperature, the substrate expands because of positive coefficients of thermal expansion in one direction, while in the perpendicular direction it shrinks due to shape memory effect overpowering thermal expansion. Consequently, the metal thin film coated on the substrate is subjected to an orthogonal compression-tension stress field and forms unidirectional wavy patterns. The experimentally obtained wrinkles are well-aligned with uniform wavelength ranging from about 930 nm to 5 μm corresponding to various programming strains and film thicknesses. A parametric study was carried out to study the influence of programming strain and film thickness on wrinkle wavelength and amplitude. The results were compared with a finite deformation model and showed good agreement with theoretical predictions. A simple analytical model incorporating a progressive damage scheme and visco-elasticity is proposed to explain defect formation and post-buckling pattern evolution, respectively. The present study is expected to offer a convenient and simple path of fabricating large-scale unidirectional wavy patterns. A potential application to organic photovoltaics is discussed.