This paper reveals the chemical, structural, and separation stability of stacked molybdenum disulfide (MoS2) membranes and establishes a low-cost and facile approach to developing stable, selective membranes for efficient molecular separation in an organic solvent. MoS2 nanoflakes that were dominant by monolayer MoS2 sheets as prepared via direct chemical exfoliation (chem-MoS2) were found to be chemically and structurally instable, with a sharp decrease in the level of solute rejection within a few days. Few-layer MoS2 nanoflakes were then fabricated using a hydrothermal method (hydro-MoS2). A "supportive" drying process involving glycerol pretreatment and drying in an oven was established to allow realignment of nanoflakes and adjustment of interflake spacing. We have shown that the hydro-MoS2 membranes provide a mean interflake free spacing of ∼1 nm, which is ideal for the separation of a model solute (Rose Bengal, size of ∼1.45 nm) from the solvent isopropanol (size of 0.58 nm) with good long-term stability over a 7 day test.