By neutron diffraction it was shown that nanostructured Se confined within a porous glass matrix exists in a crystalline as well as in an amorphous state. The spontaneous crystallization of crystalline Se from confined amorphous phase was observed. The root-mean-square amplitudes of the atomic motions in the bulk as well as in confinement are found to be essentially different in a basal plane and in the perpendicular direction along the hexagonal axis. The atomic motions in the confined Se differ from the atomic motions in the bulk at low temperatures. The results shows an unusual “freezing” of the atomic motion along the chains, while the atomic motions in the perpendicular plane still keep. This “freezing” is accompanied by the deformation of nanoparticles and the appearance of inner stresses. This effect is attributed to the interaction of confined nanoparticle with the cavity walls.