Microspheres, with diameters ranging from tens of microns to several millimeters, find extensive application in precision bearings, optical cameras, and lithography machines due to their unique mechanical and optical properties. Concurrently, the demand for improved dimensional accuracy and enhanced surface quality of these microspheres has significantly increased. As a result, the research focus has increasingly shifted towards micro-nano structuring and high-precision measurement of microspheres. In this study, an integrated device comprising a custom-developed AFM system, a control system, and proprietary software was established to achieve seamless integration of machining and measurement on the surface of microspheres. Moreover, the control system of the device has been established. The computer software is also developed based on the C++ graphical user interface (GUI) application development framework QT software. To achieve the center alignment between the micro-sphere and the air-bearing spindle, a strategy based on the device is proposed. Nanostructures, including square pit structures, triangular structures, and circular structures, are successfully machined and measured on the surface of GDP microspheres. Our findings provide a new approach for machining and measuring micro-nano structures on the surface of micro-target balls used in ICF.