We have investigated the roles of liquid crystallinity (LC) and substrate interactions on the ordering of isotropic cylindrical microdomains in thin films of two hybrid isotropic/LC triblock copolymers. Each copolymer consists of polystyrene (PS) end blocks and a side-chain LC midblock that exhibits either a nematic or smectic mesophase up to temperatures beyond the glass transition temperature (T-g) of PS. In thin films measuring on the same order as the lattice period, the orientation of the cylinders relative to the substrate is sensitive to the interactions of the mesogens at internal microdomain boundaries and external interfaces. Upon annealing such copolymer films at temperatures below the LC --> isotropic transition but above the PS T-g on a neutral NaCl substrate, the PS cylinders within the nematic matrix adopt a long-range parallel orientation, whereas those within the smectic matrix lie perpendicular to the substrate and exhibit liquidlike order. After long annealing times, the cylinders residing near the film surface within the smectic matrix reorganize from perpendicular to parallel orientation due to surface tension at the film/air interface. On a polished Si substrate that promotes homeotropic mesogen anchoring, the perpendicular cylindrical orientation within the smectic mesophase remains stable.