A comprehensive analysis and optimization of a three-dimensional integrated circuit (3D IC) structure and its thermophysical attributes are presented in this work. The thermophysical and geometrical attributes studied in this paper include the die, device layer, heat sink, and heat spreader, which are critical structures within a 3D IC. The effect of the power density of the device layer which is the source of heat generation within the chip as well as the through silicon vias (TSV) and microbumps is also considered in our investigation. The thermophysical and geometrical parameters that have a significant impact on the thermal signature of the 3D IC as well as those that have an insignificant impact were established. The comprehensive analysis of different geometrical and thermophysical attributes can guide the design and optimization of a 3D IC structure and decrease the cost.