Highly ordered liquid crystalline (LC) phases have important potential for organic electronics. We studied the molecular alignment and domain structure in a columnar LC thin film with nanometer resolution during in situ heating using four-dimensional scanning transmission electron microscopy (4D STEM). The initial disordered vapor-deposited LC glass thin film rapidly ordered at its glass transition temperature into a hexagonal columnar phase with small (<10 nm), well-aligned, planar domains (columns oriented parallel to the surface). Upon further heating, the domains coarsen via bulk diffusion, then the film crystallizes, then finally transforms back to an LC phase at an even higher temperature. The LC phase at high temperature shows straight columns of molecules, which we attribute to structure inherited from the intermediate crystalline phase. Nanoscale 4D STEM offers direct insight into the mechanisms of domain reorganization, and intermediate crystallization is a potential approach to manipulate orientational order and texture at the nano- to mesoscale in LC thin films.