Scaling up nanomanufacturing requires measuring nanoscale features fast enough to control the process. We build in-line metrology systems and the data tools that make them practical. Our roll-to-roll inspection platform integrates MEMS-based atomic force microscopes into a moving web to measure nanopatterned films during production. Fast scans are noisy, so we develop machine-learning methods that reconstruct high-resolution topography from fast, sparse measurements and remove scan artifacts. We also develop alignment metrology for holographic lithography that detects voxel-scale misalignment between metasurface-generated holograms.