Precision serial lapping in combination with raster image acquisition is an efficient and versatile approach to 3-D microstructure reconstruction of geological materials. However, during associated sample preparation and data acquisition, geometric inaccuracies are introduced, which, if neglected, severely distort the desired 3-D models of minerals and rock fabrics. A novel method is presented to assess and correct the relative shifts and rotations between the images acquired at the individual erosion levels. The method relies on optical reflection prisms which provide a precise internal reference system that allows all images making up an erosion series to be registered on a common system of coordinates. Tested on a microanalyser with digital sample stage control, the method yielded position errors between successive images of approximately 1 mu m. A thorough description of the mechanical design of the reference system and the coordinate transformation formulae are given.