Howdy!
The step-79 program uses simultaneous analysis and design (SAND) as well as second derivative information to solve this 2d problem. Most people doing large scale, 3d problems today use only first derivative information and sensitivity analysis in a nested analysis and design (NAND) context. This is because while SAND and second derivative information both allow a topology optimization program to be more robust, they also rely on a much larger system of equations.
As it is written now, the step-79 program would not work well for a 3d case, especially for high resolution. The common way to solve such a problem now would be with an "optimality criteria method" or similar.