To first order, the use of AFM as a reference tool potentially offers a large improvement over previous techniques for matching and calibration of on-line CD-SEMs. However, the utility of this approach depends on the validity of the assumption that AFM precision and accuracy are relatively constant with sample type. A full-factorial design using analysis of variations (ANOVA) has been employed in order to gauge the precision of a non-contact mode CD AFM over multiple sample types and instrument conditions. The effects of material layer, pattern geometry, feature shape, and tip size on AFM precision will be presented.