Software is among the most complex endeavors of the human mind; large scale systems can have tens of millions of lines of source code. However, seldom is complexity measured above the lowest level of code, and sometimes source code files or low level modules. In this paper a hierarchical approach is explored in order to find a set of metrics that can measure higher levels of organization. These metrics are then used on a few popular free software packages (totaling more than 25 million lines of code) to check their efficiency and coherency.