Through tapping mode atomic force microscopy and transmission electron microscopy, we were able to directly visualize the nature of crystal domains of liquid crystalline poly(3,3'''-dialkylquaterthiophene) in its spin-coated films. The size of domains, consisting of large anisotropic lamellar stacks formed by arrays of pi-pi stacking polymer chains, was highly dependent on annealing temperature covering the range from the crystal-to-liquid crystal to the liquid crystal-to-isotropic phase transitions. After annealing at the melting temperature, slow cooling gave rise to close packing of parallel lamellar stacks within the domain, while fast cooling led to clear separation of lamellar stacks. The surface modification of the substrate was particularly critical to the orientation of these domains of lamellar stacks: the SiO2-surface modified with octyltrichlorosilane led to lamellar stacking domains oriented with their lamellar axes normal to the modified surface.