We develop a formal approach to design shaped microstructures from multilayer films with eigenstrains in the layers. The eigenstrains are inelastic strains that vary from layer to layer resulting in elastic misfit between the layers. Examples include thermal expansion mismatch between the layers, piezoelectric strains, and strains in shape memory alloys. In our approach, the eigenstrains are manipulated by spatially patterning the films to generate structures that, although fabricated by a conventional, planar thin film technology, deform into desired three-dimensional shaped surfaces. The material patterns in the individual layers are determined by topology optimization allowing the creation of arbitrarily complex, geometric layouts. In contrast to existing topology optimization methods for patterning plate structures, the goal of the proposed approach is to generate large deformations via eigenstrains, rather than to increase the stiffness of plate via reinforcement patterns. The optimization methodology is demonstrated by the design of two-and three-layer thin film structures. The performance of the optimized designs is verified by experiments showing the importance of accounting for a nonlinear kinematics in order to obtain the desired shape in the deformed configuration. While our approach is demonstrated in the context of the design of three-dimensional microstructures, it can be easily applied to a variety of problems where it is desired to control the complex shape of plate-like structures by spatial actuation-the spatial actuators are represented by eigenstrains.