Abstract: In the process of micro-nano machining, samples often need to be sputtered and cut by focused ion beam (FIB), and characterized by scanning electron microscope (SEM) and atomic force microscope (AFM). Samples need to be fixed on the sample table before tested by these three instruments. However, poor fixation will affect the characterization results, but the firmly fixed samples are easy to be destroyed in the process of transfer, disassembly and re-fixation between different instruments. Based on the above problems, the AFM-SEM-FIB sample co-positioning system was designed, which could realize non-destructive transfer and co-positioning of samples between the three instruments, and avoid the precious samples destruction and loss of targets. And the problems were solved that AFM scanning cannot control the direction and quickly adjust the location. With excellent performance in micro-nano characterization, the system has been developed into products and sold in large quantities.