Three dimensional vertically integrated systems allow active devices to be placed on multiple device layers. In recent years, a number of research efforts have addressed physical synthesis issues for such systems. Such efforts showed a significant reduction in interconnect lengths. In order to effectively synthesize designs for 3D systems, it is necessary to take layer assignment for resources into considerahigher levels of the design abstraction. We address the layer assignment problem as a part of a physical aware behavioral synthesis flow. We propose a 0-1 linear program formulation to perform simultaneous and optimal scheduling, binding and layer assignment for synthesizing designs for three-dimensional vertically integrated systems. The objective is to minimize inter-stratal via and the interconnect length in the critical path while taking thermal gradient between layers into account (which has been shown to be of particular concern for 3D systems). Floorplanning is performed f...