Abstract: A capsule surface profiler system based on vertical spindle structure and atomic force microscope (AFM) was developed, and its systematic measurement tests were carried out. In order to evaluate the measurement uncertainty, the experimental studies mainly included the air-bearing spindle rotation run out error test, the system static noise test, and the comprehensive test. The rotary precision of air bearing was tested and the error curve of the spindle was obtained with a standard ball and two-step separation method. Further, this error curve was eliminated as in a systematic error. Comprehensive measurement tests of the system prove that the noise peak value of this system is about 22 nm and its RMS is about 5.2 nm during the measurement process.