The task of 3D ICs layout design involves the assembly of millions of components taking into account many different requirements and constraints such as topological, wiring or manufacturability ones. It is a NP-hard problem that requires new non-deterministic and heuristic algorithms. Considering the time complexity, the commonly applied Fiduccia-Mattheyses partitioning algorithm is superior to any other local search method. Nevertheless, it can often miss to reach a quasi-optimal solution in 3D spaces. The presented approach uses an original 3D layout graph partitioning heuristics implemented with use of the extremal optimization method. The goal is to minimize the total wire-length in the chip. In order to improve the time complexity a parallel and distributed Java implementation is applied. Inside one Java Virtual Machine separate optimization algorithms are executed by independent threads. The work may also be shared among different machines by means of The Java Remote Method Invocation system.