Micropatterned phospholipid bilayers on solid substrates offer an attractive platform for various applications, such as high throughput drug screening. We have previously developed a photopolymerization-based methodology for generating micropatterned bilayers composed of polymerized and fluid lipid bilayers. Lithographic photopolymerization of a diacetylene-containing phospholipid (DiynePC) allowed facile fabrication of compartmentalized arrays of fluid lipid membranes. Herein, we report on a key experimental parameter that significantly influences the homogeneity and quality of the fabricated polymeric bilayers, namely the temperature at which monolayers of monomeric DiynePC were formed on the water surface and transferred onto solid substrates by the Langmuir-Blodgett/Langmuir-Schaefer (LB/LS) technique. Using fluorescence microscopy and atomic force microscopy, it was found that polymerized bilayers were homogeneous, if bilayers of DiynePC were prepared below the triple point temperature (ca. 20 C) of the monolayer, where a direct transition from the gaseous state to the liquid condensed state occurred. Bilayers prepared above this temperature had a markedly increased number of crack-like line defects. The differences were attributed to the domain structures in the monolayer that were transferred from the water surface to the substrate. Domain size, rather than the molecular packing in each domain, was concluded to play a critical role in the formation of defects. The spontaneous curvature and area changes of bilayers were postulated to cause destabilization and detachment of the films from the substrate upon polymerization. Our present results highlight the importance of controlling the domain structures for the homogeneity of polymerized bilayers required in technological applications.