International SEMATECH (ISMT) and the National Institute of Standards and Technology (NIST) are working together to improve the traceability of AFM dimensional metrology in semiconductor manufacturing. Due to the unique metrology requirements and the rapid change in the semiconductor industry, relevant standards are often not available. Consequently, there is often no traceable linkage between the realization of the SI (Systeme International d’Unites, or International System of Units) unit of length -- the meter -- and measurements in the fab line. To improve this situation, we have implemented a Reference Measurement System (RMS) using a next-generation critical-dimension atomic force microscope (CD-AFM). We performed measurements needed to establish a traceability chain and developed uncertainty budgets for pitch, height, and critical dimension (CD) measurements. At present, the standard uncertainties are estimated to be approximately 0.2% for pitch measurements, 0.4% for step height measurements, and 5 nm for CD measurements in the sub-micrometer range. Further improvement in these uncertainties is expected with the use of newer samples for scale and tip calibration. We will describe our methodology for RMS implementation and the major applications for which it has been used. These include measurements on new NIST/ISMT linewidth standards, a reference tool for CD-scanning electron microscopes (SEMs), metrology on photo-masks, CD-SEM benchmarking, and 193 nm resist shrinkage measurements. As part of the NIST/ISMT linewidth standards project, we are performing an extensive comparison experiment of AFM and TEM (transmission electron microscopy) measurements of linewidth.