The enantioselective solid-solid clathration of (S)-pantolactone ( I ) into (R,R)-trans-2,3-bis(diphenylhydroxymethyl)-l,4-dioxaspiro[4~4]nonane (2) and -[4.5]decane (3) was studied preparatively and mechanistically using atomic force microscopy (AFM) measurements and crystal packing data. Shortdistance solid-to-solid sublimation mechanisms occur in both cases with initial formation of epitaxial floes along the b-axis in 2 and random craters in 3. The bulk control in the phase rebuilding stage is understood from the particular crystal packings. Bulk control was largely lost in the phase transformation stage when passivation of the surfaces occurred in both cases. The host lattices of 2 and 3 exhibit closed molecular double layers with all hydroxyl groups inside and lacking access for intercalation of I. The reaction has to start at isolated surface defects. Once started, new doors for further entrance of guest molecules (S)-I are opened in the double layer. For practical use, both the crystallographic difficulties and the passivation have to be overcome. A slurry technique involving addition of stoichiometric amounts of water to the solids provided useful conditions for the preparative resolution of (R/S)-I or further racemates exhibiting passivation, whereas heating alone speeded up the resolution of 2-methylpiperwine with 2.