A linear stability analysis is presented for the contact instability of a soft thin elastic film which is rigidly bonded to a physically patterned substrate, and is in adhesive contact with a smooth rigid contactor. Increasing roughness by enhancing the substrate-amplitude produces increasingly smaller instability length-scales. The smallest wavelengths obtainable are 0.3*h, an order of magnitude smaller than that observed with films on flat substrates (3*h). Instability length-scales are found to be largely independent of substrate length-scales. For van der Waals interaction, increase in substrate roughness increases the energy penalty and, consequently, requires smaller gap distances (1nm for stiff films) to engender instabilities. When an externally controllable long-range electric field is employed instead, instabilities can be initiated at very low critical voltages (32V) even in relatively stiff films, making it a more suitable route to produce miniaturized instability patterns.