This paper presents a novel three-dimensional (3D) thermal simulation tool for semiconductor integrated devices. The simulator is used to automatically generate an accurate 3D physical model of the device to be simulated from layout information. The simulator produces an appropriate mesh of the device based on a rectangular block structure. The mesh is automatically created such that a fine mesh is produced around heat generation regions, but a moderate number of blocks are used for the entire device. This paper first confirms that the simulator produces an accurate solution to the nonlinear differential equation describing the heat flow. Then model generation from three example technologies (silicon trench, GaAs mesa structures, silicon on insulator) is presented. The potential of the simulator to quickly and easily explore the effect of layout and process variations is illustrated, with the simulation of a two-transistor GaAs power cell as a large example. The program incorporates a transient solver based on a transmission line matrix (TLM) implementation using a physical extraction of a resistance and capacitance network. The formulation allows for temperature dependent material parameters and a nonuniform time stepping. An example of a full transient solution of heat flow in a realistic Si trench device is presented.