In 2004, the National Institute of Standards and Technology (NIST) commissioned the Advanced Measurement Laboratory (AML) -a state-of-the-art, five-wing laboratory complex for leading edge NIST research. The NIST NanoFab -a 1765 m 2 (19 000 ft 2 ) clean room with 743 m 2 (8000 ft 2 ) of class 100 space -is the anchor of this facility and an integral component of the new Center for Nanoscale Science and Technology (CNST) at NIST.Although the CNST/NanoFab is a nanotechnology research facility with a different strategic focus than a current high volume semiconductor fab, metrology tools still play an important role in the nanofabrication research conducted here. Some of the metrology tools available to users of the NanoFab include stylus profiling, scanning electron microscopy (SEM), and atomic force microscopy (AFM).Since 2001, NIST has collaborated with SEMATECH to implement a reference measurement system (RMS) using critical dimension atomic force microscopy (CD-AFM). NIST contributed traceable metrology expertise and SEMATECH provided access to leading edge metrology tools in their facilities. Now, in the newly launched "clean calibrations" thrust at NIST, we are implementing the reference metrology paradigm on several tools in the CNST/NanoFab. Initially, we have focused on calibration, monitoring, and uncertainty analysis for a three-tool set consisting of a stylus profiler, an SEM, and an AFM.Our goal is the development of new and supplemental calibrations and standards that will benefit from the Class 100 environment available in the NanoFab and offering our customers calibration options that do not require exposing their samples to less clean environments. We have completed a preliminary evaluation of the performance of these instruments. The results suggest that the achievable uncertainties are generally consistent with our measurement goals.