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In this paper, we describe a novel interleaved scanner for an eye-safe 3D scanning lidar system to measure aerodynamic phenomena in a wind tunnel using elastic backscatter from seeding particles. The scanner assembly consists of a rotating polygon scanner for line scanning along the fast axis, a galvanometer (galvo) scanner for scanning along the slow axis, angular position sensors and motor controllers. The polygon scanner sweeps the lidar beam at up to 10,000 lines/s across a 27 deg angular field-of-regard in the fast axis, while the galvo scanner covers an angular range of 20 deg in the slow axis. Using this scanner, the lidar can perform non-intrusive flow visualization, velocimetry, and hard target mapping at mmscale spatial resolution to a standoff range of 5 m at an update rate of 50 Hz for the full field-of-regard. An interleaved scanning methodology for the acquisition of two snapshots of 3D lidar intensity data with a 100 μs time offset is discussed. The design of the control and data acquisition electronics is described. The effects of rapid scanning on the response of a narrow field-of-view lidar are addressed. The design of the scanner is scalable and can be tailored to meet the requirements of other applications by increasing or decreasing the standoff range, angular field-of-regard and scan rate.