The ccc stereoisomer-purified tert-butoxycarbonyloxy-protected calix[4]resorcinarene molecular resists blended with photoacid generator exhibit a non-uniform photoacid-catalyzed reaction in thin films. The surface displays a reduced reaction extent, compared with the bulk, with average surface-layer thickness 7.0 ± 1.8 nm determined by neutron reflectivity with deuterium-labelled tert-butoxycarbonyloxy groups. Ambient impurities (amines and organic bases) are known to quench surface reactions and contribute, but grazing-incidence X-ray diffraction shows an additional effect that the protected molecular resists are preferentially oriented at the surface, whereas the bulk of the film displays diffuse scattering representative of amorphous packing. The surface deprotection reaction and presence of photoacid were quantified by near-edge X-ray absorption fine-structure measurements.