The ongoing miniaturization in micro- and nanotechnology requires multi-physical characterization methods on the same small scale as the materials and components are. Although many characterizations systems exist, only few approaches allow to gather several different types of information collaboratively. Furthermore, functional building blocks and devices working on the nanoscale, have to be characterized and tuned during the manufacturing process. This can be done with combined microscopic and processing systems. A software framework, which controls and acquires all units and data, is engaged and allows combined analysis and automation. This combination approach is demonstrated by several applications in microscopy, manipulation and automation on the small scale.