Three cyclopentadithiophene-difluorophenylene copolymers (named PhF2,3, PhF2,5, and PhF2,6), which differ by the arrangement of fluorines on the phenylene structural unit, were designed and synthesized for the fabrication of organic field-effect transistors (OFETs). Single crystal structures of model compounds representative of the backbone and density functional theory (DFT) were used to estimate the backbone shape for each copolymer. The different substitution arrangements impact the backbone secondary structure through different nonbonding F···H interactions. PhF2,5 and PhF2,6 assumed more linear backbones relative to PhF2,3, which in turn impacts self-assembly and polymer chain alignment on nanogrooved (NG) substrates. A larger improvement of charge carrier mobility for the more linear backbones was achieved when using NG substrates. Among the three polymers, PhF2,6 achieved the highest average field-effect hole mobility (5.1 cm2 V-1 s-1). As evidenced by grazing incidence wide-angle X-ray scattering (GIWAXS), thin films of PF2,5 and PF2,6 exhibited a higher degree of anisotropic alignment, relative to the more curved PF2,3 counterpart, consistent with the higher hole mobilities. This work gives insight into how nonbonding interactions can influence charge carrier mobility through changes in secondary structure and suggests that polymers with more linear shapes might be preferred for achieving greater levels of alignment within the confines of a NG environment.