Integrated nanopatterns were successfully obtained from a combination of high lateral ordering of newly designed self-assembling fluorine-containing block copolymers and degradation of the fluorine-containing polymer nanodomains in e-beam irradiated areas. The fluorine-containing block copolymers of poly(styrene-block-2,2,2-trifluoroethyl methacrylate) (PS-b-PTFEMA) and poly[styrene-block-(methyl methacrylate-co-2,2,2-trifluoroethyl methacrylate)] (PS-b-(PMMA-co-PTFEMA)), which are capable of both top-down and bottom-up lithography, were developed. The reported block copolymers were synthesized by either anionic polymerization or atom transfer radical polymerization (ATRP). Characterization of bulk and thin films were carried out using differential scanning calorimetry (DSC), transmission electron microscopy (TEM), and small-angle X-ray scattering (SAXS), and these studies revealed the formation of highly ordered self-assembled structures. Lateral ordering of arrays of PS dots was observed in the thin film of PS-b-PTFEMS, in which PS was the minor block, and the thin film of PS-b-(PMMA-co-PTFEMA), in which PS was the major block. These thin films were subjected to conventional lithographic processing using e-beam and deep-UV radiation to create integrated patterns such as “dots in lines”.