Thin heteroepitaxial overlayers have been proposed as templates to generate stable, self-organized nanostructures at large length scales, with a variety of important technological applications. However, modeling strain-driven self-organization is a formidable challenge due to different length scales involved. In this Letter, we present a method for predicting the patterning of ultrathin films on micron length scales with atomic resolution. We make quantitative predictions for the type of superstructures (stripes, honeycomb, triangular) and length scale of pattern formation of two metal-metal systems, Cu on Ru(0001) and Cu on Pd(111). Our findings are in excellent agreement with previous experiments and call for future experimental investigations of such systems.