Manufacturing control systems in the future will be facilitated by multi-technological solutions, families of products based on some basic sets of solutions, and updates and configurations for customisation. Exact and verified specifications are of key importance when considering the effectiveness of design work. A study on the software development for a very flexible manufacturing system, `holonic' system is reported here. The overall system analysis is guided with well-defined functional architecture, called PEM-modelling, to provide consistency and cohesion in the system structures. The software development is carried out following the principles of object oriented analysis and design with CASE tools providing methods for exact definitions and fast software development.