Workhorse metrology such as CD-SEM is used during process development, process control, and optical proximity correction model generation and verification. Such metrology needs to be calibrated to handle various types of profiles encountered during IC fabrication. Reference metrology is used for calibration of workhorse metrology. There is an astounding need for sub-half and sub-quarter nanometer measurement uncertainty in the near future technology nodes as envisaged in the International Technology Roadmap for Semiconductors. In this regime of desired measurement uncertainty all metrology techniques are deemed limited and hybrid metrology appears promising to offer a solution. Hybrid metrology is the use of multiple metrology techniques, each with particular strength, to reduce the overall measurement uncertainty. CD-AFM makes use of a flared probe in order to scan the sidewalls and bottom of the pattern on a wafer to provide 3D profile and CD measurements at desired location on the profile. As the CD shrinks with technology nodes especially the space, the size of the AFM probe also needs to shrink while maintaining the flared geometry specifications. Unfortunately the fabrication of such probes is a challenge and new techniques are required to extend reference metrology to the smallest space and hole of interest. This paper proposes a reference system combining CD-AFM and patterning simulation model. This hybrid metrology system enables CD metrology in a space not measurable directly by conventional CD-AFM probe. The key idea is to use the successfully measured profile and CD information from the CD-AFM to calibrate or train the patterning simulation optical and resist model. Ability of this model to predict profile and CD measurement is verified on a physically measured dataset including cross sections and additional CD-AFM measurements. It is hypothesized that this model will be able to predict profile and CD measurements in otherwise immeasurable geometries. Being based on optics and materials fundamentals, this approach is presumed to be more accurate compared to mere extrapolation approach in use today. We report on the measurement uncertainty improvement with this approach. Situations with highest prediction confidence involve CD-AFM scanning resulting in partial information. For example, using carbon nanotube probes or CDP where there is little flaring of the tip, the CD-AFM cannot detect significant undercutting of the structure. Achieving agreement with the calibrated patterning model for measurement metrics such as height, top and middle CD permits the prediction of the bottom CD to be used as an authentic reference measurement. © 2010 Copyright SPIE - The International Society for Optical Engineering.