Liquid-crystalline polymers with maleic acid anhydride moieties in the backbone and methoxybiphenyl groups in the side chain have been investigated with respect to the ordering in and stability of thin films on chemically modified silicon substrates. For unmodified silicon wafers, it is known that the polymer-substrate interaction induces parallel layering in the film, resulting in rather stable films. When the surface groups are changed, i.e., by silylation, the interaction between the polymer and the surface can be tuned. This results in unstable films with a dewetting behavior that is strongly temperature and substrate dependent. At low temperatures in the mesophase holes nucleate, which are encircled by unstable rims. Upon annealing at higher temperature the rim instability decreases and the dewetting velocity increases. This feature also occurs for another completely different side-chain liquid-crystalline polymer with a methacrylate backbone and cyanobiphenyl groups in the side chains. We ascribe the peculiar dewetting behavior to the presence of polycrystalline domains in the thin films. Especially their size and orientation and their ability to deform under shear are held responsible for the rim instabilities and, consequently, for the droplets remaining behind in the dry patches.