Stationary states of a single-walled carbon nanotube array lying on a flat substrate formed by the surface of a molecular crystal are investigated. Numerical modeling showed that in the case of weak interaction with the substrate it is more energetically favorable for nanotubes to get assembled into multilayer packing, while in the case of strong interaction (e.g., the interaction with the h–BN crystal surface) they form monolayer packing (i.e., a chain on the substrate surface). The dynamics of nanotube chains is modeled. We show that acoustic supersonic solitons can exist only in small-diameter nanotubes (D < 0.8 nm), and soliton motion is always accompanied by energy loss to excitation of internal vibrations in nanotubes. Low-amplitude vibrations are analyzed. For a finite nanotube chain residing on a flat substrate, it is shown that vibrations are confined to only the end nanotubes or a nanotube that forms a structural defect in the chain.