To create composite synthetic scaffolds with the same degree of complexity and multilevel organization as biological tissue, we need to integrate multilevel biomaterial processing in rapid prototyping systems. The scaffolds then encompass the entire range of properties, which characterize biological tissue. A multilevel microfabrication system, PAM(2), has been developed to address this gap in material processing. It is equipped with different modules, each covering a range of material properties and spatial resolutions. Together, the modules in PAM(2) can be used to realize complex and composite scaffolds for tissue engineering, bringing us a step closer to real clinical applications. This chapter describes the PAM(2) system and discusses some of the practical issues associated with scaffold microfabrication and biomaterial processing.