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We present HiRA-Pro, a novel procedure to align, at high spatio-temporal resolutions, multimodal signals from real-world processes and systems that exhibit diverse transient, nonlinear stochastic dynamics, such as manufacturing machines. It is based on discerning and synchronizing the process signatures of salient kinematic and dynamic events in these disparate signals. HiRA-Pro addresses the challenge of aligning data with sub-millisecond phenomena, where traditional timestamp, external trigger, or clock-based alignment methods fall short. The effectiveness of HiRA-Pro is demonstrated in a smart manufacturing context, where it aligns data from 13+ channels acquired during 3D-printing and milling operations on an Optomec-LENS® MTS 500 hybrid machine. The aligned data is then voxelized to generate 0.25 second aligned data chunks that correspond to physical voxels on the produced part. The superiority of HiRA-Pro is further showcased through case studies in additive manufacturing, demonstrating improved machine learning-based predictive performance due to precise multimodal data alignment. Specifically, testing classification accuracies improved by almost 35% with the application of HiRA-Pro, even with limited data, allowing for precise localization of artifacts. The paper also provides a comprehensive discussion on the proposed method, its applications, and comparative qualitative analysis with a few other alignment methods. HiRA-Pro achieves temporal-spatial resolutions of 10-1000 𝜇s and 100 𝜇m in order to generate datasets that register with physical voxels on the 3D-printed and milled part. These resolutions are at least an order of magnitude finer than the existing alignment methods that employ individual timestamps, statistical correlations, or common clocks, which achieve precision of hundreds of milliseconds.