The National Institute of Standards and Technology (NIST) has provided industry with a scanning electron microscope (SEM) magnification calibration sample Reference Material (RM) 8090. The certified, Standard Reference Material (SRM) version, SRM 2090 is currently being prepared for issuance. This paper describes the design and development of a new, PC-based measurement and control system developed to facilitate the certification of the SRM 2090 artifact samples in a specialized metrology microscope. SRM 2090 is certified by moving the sample under a finely focused stationary electron beam in the metrology electron microscope. Using a laser interferometer with displacement measurements traceable to basic wavelength standards, the motion is measured while recording the secondary or backscattered electron output signal. A computer controls the motion, records the signal and interferometer value, then calculates the accurate spacing of the features, completes the statistical work and generates the NIST certificate. The original measurement system design was developed in the early 1990s. This paper outlines the effort to upgrade the system, including the replacement of the outdated measurement and control system with a new, LabVIEW based measurement and control system. The details of the new measurement and control system will be discussed and results will be presented.