Dense arrays of high-aspect-ratio (HAR) vertical nanostructures are essential elements of microelectronic components, photovoltaics, nanoelectromechanical, and energy storage devices. One of the critical challenges in manufacturing the HAR nanostructures is to prevent their capillary-induced aggregation during solution-based nanofabrication processes. Despite the importance of controlling capillary effects, the detailed mechanisms of how a solution interacts with nanostructures are not well understood. Using in situ liquid cell transmission electron microscopy (TEM), we track the dynamics of nanoscale drying process of HAR silicon (Si) nanopillars in real-time and identify a new mechanism responsible for pattern collapse and nanostructure aggregation. During drying, deflection and aggregation of nanopillars are driven by thin-liquid-film instability, which results in much stronger capillary interactions between the nanopillars than the commonly proposed lateral meniscus interaction forces. The importance of thin-film instability in dewetting has been overlooked in prevalent theories on elastocapillary aggregation. The new dynamic mechanism revealed by in situ visualization is essential for the development of robust nanofabrication processes.