The free surface of a soft elastic film becomes unstable and forms an isotropic labyrinth pattern when a rigid flat plate is brought into adhesive contact with the film. These patterns have a characteristic wavelength, lambda similar to 3H, where H is the film thickness. We show that these random structures can be ordered, modulated, and aligned by depositing the elastic film (cross-linked polydimethylsiloxane) on a patterned substrate and by bringing the free surface of the film in increasing adhesive contact with a flat stamp. Interestingly, the influence of the substrate "bleeds" through the film to its free surface. It becomes possible to generate complex two-dimensional ordered structures such as an array of femtoliter beakers even by using a simple one-dimensional stripe patterned substrate when the instability wavelength, lambda similar to 3H, nearly matches the substrate pattern periodicity. The free surface morphology is modulated in situ by merely varying the stamp-surface separation distance. The free surface structures originating from the elastic contact instability can also be made permanent by the UV-ozone induced oxidation and stiffening. (c) 2007 American Institute of Physics.