Solvent vapor annealing (SVA) for polymer treatment is widely used for manufacturing organic photovoltaic devices, but the process is poorly understood on the microscopic scale. In this study, an optical monitoring system is designed and used to perform real‐time fluorescence analysis of dispersed poly(3‐hexylthiophene) (P3HT) and para‐phenylene ethynylene (PPE) films during SVA. The initial swelling of aggregates occurs within seconds. Chain rearrangements then occur and an equilibrium state is reached within minutes. Surface morphologies for both P3HT and PPE polymers are examined using atomic force microscopy (AFM) before and after the SVA process. Although similar transformations from random globules to micrometer‐scale nanowires are observed for both polymers, P3HT forms nanowires more easily and quickly than PPE does. The higher solubility of P3HT in chloroform results in superior long‐range order; by contrast, PPE chains align into nanowires only with sufficient free space. Real‐time spectroscopic monitoring of structures and morphological characterization of such structures through AFM during SVA can improve the understanding of how polymer chains rearrange into ordered structures.