This study aims to explore the structural characteristics of the inhomogeneous top layer of thin-film composite membranes when pretreated by different methods: room temperature-oven, ethanol-hexane in a solvent exchange process, and freeze-drying. An evaluation of the nano-order free-volume pore size of the polyamide samples was carried out by nanopermporometry (NPP) and was quantitatively compared with the free-volume pore estimated from normalized Knudsen-based permeance (NKP) and with positron annihilation characterization (PALS). NPP results denoted a bimodal polyamide membrane structure described by a dense matrix and highly permeable regions. The application of different condensable vapors (water, hexane, and isopropanol) resulted in a free-volume pore size smaller than d(p) = 0.6 nm for dense regions, which was confirmed after NKP and PALS. In addition, the influence of highly permeable regions on permeance decreased in the following order: ethanol hexane > freeze-drying > room temperature oven samples, demonstrating an effective membrane structure alteration after different pretreatments.