A system and method of scanner characterization is provided which establishes an accurate relationship between a scanner's device-dependent (scanner) color space and a device-independent colorimetric space. A hierarchical subdivision of device-dependent color space into sub-regions is performed. The sub-regions are defined by cutting planes dividing patch color values in device-dependent color space perpendicular to principal axes. A color transformation matrix is then generated establishing the relationship between the scanner device-dependent color space and the device-independent color space for each sub-region of device-dependent color space using the patch color values and a weighting function for each matrix. Each weighting function gives a weight to each patch color value which is a function of the location of the patch color value with respect to the cutting planes defining the sub-region containing the patch color value.