Mobility of molecules in confined geometry has been studied extensively, but the origins of finite size effects on reduction of the glass transition temperature, T(g), are controversial especially for supported thin films. We investigate uptake of probe molecules in vapor-deposited thin films of cumene, 3-methylpentane, and heavy water using secondary ion mass spectrometry and discuss roles of individual molecular motion during structural relaxation and glass-liquid transition. The surface mobility is found to be enhanced for low-density glasses in the sub-T(g) region because of the diffusion of molecules on pore walls, resulting in densification of a film via pore collapse. Even for high-density glasses without pores, self-diffusion commences prior to the film morphology change at T(g), which is thought to be related to decoupling between translational diffusivity and viscosity. The diffusivity of deeply supercooled liquid tends to be enhanced when it is confined in pores of amorphous solid water. The diffusivity of molecules is further enhanced at temperatures higher than 1.2-1.3 T(g) irrespective of the confinement.