Abstract: Method for generating a three dimensional image of a sample of a material on a micrometer length scale comprises disposing the sample of the material on a sample holder, moving the sample holder to a first location where a tool is moved in a first direction toward the sample to remove material from the sample to provide a sample cross-section, moving the sample holder in a second direction to a second location where a digital image of the sample section is generated and stored, sensing the position of the sample holder at the second direction and storing the sensed position associated with the digital image, repeating steps a) through d) to provide a series of digital images and a corresponding series of sensed positions, and constructing a three dimensional image of the sample using the series of digital images and the corresponding series of sensed positions.