Because of their high quality, repeatability, and non-destructive nature, CD-SEMs are the gold standard for metrology in the fab. Yet, there are known offsets from this metrology type compared to others. For example, there is an inherent bias in the measurements made on the top down CD-SEM relative to measurements made from cross-sections. The underlying causes for this bias are complex, and are related both to the measurement techniques used and the interpretation of the data in terms of a specific measurement model. In extracting a line width measurement from a CD-SEM line-scan, for example, the line-scan analysis algorithm interacts with the resist profile shape to produce reported CD. The influence of the resist profile shape on the CD for top down measurements will, in general, be different from the influence of profile shape on a cross-sectional measured CD. We present here a study of CD metrology made with top down CD-SEMs and the corresponding cross-sectional metrology taken from the same structures on the same wafers. The experimental data show the top-down to cross-section offsets to be small, but present over a variety of profile shapes and measurement algorithms. We then use a simple simulation of a typical CD-SEM measurement to predict the offset as a function of beam properties, material composition, and profile shape of the structures being measured. We compare our simulations with the experimental data, tuning the model to give accurate results for our test structures. In this manner, we hope to adequately predict the top-down offset and thereby eliminate it as a source of error in calibrating a lithography simulator.