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Super-resolution fluorescence microscopy is used for the first time to study the nanoscale kinematics of a MEMS device in motion across a surface. A device under test is labeled with fluorescent nanoparticles that form a microscale constellation of near-ideal point sources of light. The constellation is imaged by widefield epifluorescence microscopy, and the image of each nanoparticle is fit to a Gaussian distribution to calculate its position. Translations and rotations of the device are measured by computing the rigid transform that best maps the constellation from one image to the next. This technique is used to measure the stepwise motion of a scratch drive actuator across each of 500 duty cycles with 0.13-nm localization precision, 1.85-nm displacement uncertainty, and 100-μrad orientation uncertainty for a constellation diameter of 15 μm. This novel measurement reveals acute aperiodic variations in the step size of the actuator, which have been neither previously observed nor predicted by any of the published models of the operation of the device. These unexpected results highlight the importance of super-resolution fluorescence microscopy to the measurement of MEMS kinematics, which will have broad impact in fundamental investigations of surface forces, wear, and tribology in MEMS and related applications.