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In this paper we present a general design methodology suitable for a class of complex multi-agent systems which are capable of self-assembly. Our methodology is based on a top-down, bottom-up approach, which has the potential to achieve a range of global design goals whilst retaining emergent behaviour somewhere in the system, and thereby allowing access to a richer solution space. Our experimental environment is a software system to model 2-dimensional self-assembly of groups of autonomous agents, where agents are defined as square smart blocks. The general design goal for such systems is to direct the self-assembly process to produce a specified structure. The potential of this design methodology has been realised by demonstrating its application to a “toy” problem – the self-assembly of rectangles of different sizes and shapes in a two-dimensional mesoblock environment. The design procedure shows different choices available for decomposing a system goal into subsidiary goals, as well as the steps needed to ensure a match to what is achievable from the bottom-up process. Encouraging results have been obtained, which allows mesoblock rectangles of specified size to be assembled in a directed fashion. Two different approaches to the same problem were presented, showing the flexibility of the method.