Looking at the graphic result of a material flow analysis (MFA), it seems easy and straightforward to define the system, collect the data, calculate the results, and draw conclusions. In practice, one does not start with the result but quite often with a badly defined problem that is highly complex and that has to be simplified and well structured first. After the goals of an MFA have been clearly defined, the real art consists of skillfully designing a system of boundaries, processes, flows, and stocks that allows solving a given problem at the least cost. Like in any other art, a precondition for mastering the art is to exercise the basic tools as much as possible. The more experienced a user gets, the easier it becomes to set up an appropriate system in a cost-effective way. An expert skilled in MFA will be able to define a metabolic system in any new field quite efficiently, with only a few alterations of the initial draft. Beginners will often find out that they have to revise their systems several times in order to cope with facts such as incomplete information about the important processes, stocks, and flows within the system; inappropriate systems boundaries; missing, bad, or incompatible data; etc.