In a sample analysis method, positional coordinates of reference points on a surface of the sample are measured using a first device. Positional coordinates of an object on the surface of the sample to be analyzed are also measured using the first device. A sample piece containing on a surface thereof a preselected number of the reference points and the object is removed from the sample. The sample piece is then mounted on a second device different from the first device. The positional coordinates of the reference points on the surface of the sample piece are then measured using the second device. The positional coordinates of the object on the surface of the sample piece are then calculated using the positional coordinates of the reference points measured by the second device and the positional coordinates of the object measured by the first device. The object on the surface of the sample piece is then analyzed.