The fabrication of liquid crystal display (LCD) panels involves several thermal processes such as imidization of the alignment layer (AL) and annealing of the rubbed polyimide AL. The nature of these processes on the LC alignment, especially on the pretilt angle (Θ$\_$p/) has been systematically studied, employing various types of polyimide structures. The imidization effect depends on the nature of polyimid precursors; Θ$^$p/ increases with the degree of the imidization for the main-chain type of ALs, due to the decrease in the surface polarity, but this relation is not applicable to the alkylated ones in which the steric effect at the AL surface by the aliphatic side chains is dominant. Annealing of the rubbed polyimide AL deteriorates its rubbing-induced molecular orientation and subsequently the overlying LC alignment, resulting in the decrease in Θ$\_$p/. Especially, annealing of the LC cell affects the LC-AL interaction as well as the AL orientation and thus its effect on LC alignment depends sensitively on the nature of LC-polyimide interface; aromatic moiety in the polyimide structure gives better thermal stability of LC alignment while fluorinated polyimide ALs induce the less stable alignment.