Here we present time-resolved in situ transmission electron microscopy (TEM) observations and real-time manipulation of nematic ordered cellulose and ultradrawn polyethylene films. Drawn films of these two polymers exhibited a unique response to the low-dose electron beam. Electron beam damage was minimal based on retention of an organized electron diffraction pattern. Increased electron dosage appeared to melt the polymer with subsequent movement and attraction toward preferred electron concentrations within the beam. This discovery allowed the preferential, directed manipulation of polymer chain aggregates in two dimensions. These findings provide a basis for a new technique to manipulate and simultaneously observe dynamic assembly at the molecular level of structures using TEM.