Instrumentation used for nanotechnology such as the scanning tunneling microscope (STM) and the atomic force microscope (AFM) can also be applied for biological and biomedical applications. Rapid progress in this research area has allowed nanometer-scale imaging and functional studies of single cells, proteins, and DNA under physiological conditions. In nanotechnology, the traditional scientific approach is primarily based on computers for modeling, simulation, etc., and on instrumentation or tools for experimentation, characterization, synthesis, and many more. Although the throughput in computation has increased at an excessively high pace following Moore's law (doubling every 18 months), today's researchers involved in nanotechnology are still using tools such as single-tip conventional scanning probe microscopes (SPMs) such as the STM or the AFM that have throughput still comparable to the first STM developed more than 20 years ago. History tells us that throughput in instrumentation is very often a determining factor in research and development. For instance, researchers initially performed DNA sequencing by hand. As scientists began to find new applications for DNA analyses, the demand for faster and more efficient technology increased. To prepare for the future, we are developing a revolutionary high-throughput instrumented platform for accelerating many research activities and applications in nanotechnology. The approach used is designed to be adapted for a number of different types of automated research tasks and operations-from measuring and manipulating molecules to developing new pharmaceuticals by testing molecules against potential drug targets. The point is to have a versatile device that can be used for many different types of research. As such, our approach leads to the development and the use of miniature scientific instruments configured as autonomous miniature robots. To provide a simple example, our present design allows for more than one hundred of these robots to work on a single half-meter diameter platform, allowing for more than 20,000,000 STM-based measurements per second. Because such throughput cannot be handled in real- time by one or more researchers, the project naturally leads to tools to automate the scientific method itself where an entire program of research may be carried out by one machine as opposed to a building full of separate machines. The talk will give the present status and the main engineering challenges in developing such type of platform that could potentially be used in future high-throughput biomedical research activities.