The structures of the spin-coated poly(3-dodecylthiophene) [P3DDT] thin films along the out-of-plane and in-plane directions, and the influence of solvent vapor annealing and thermal annealing on their structures, which are of immense importance for their performance as semiconducting materials, were investigated using complementary X-ray reflectivity and atomic force microscopy techniques. The P3DDT films of different thicknesses (~3.4 nm, i.e. ‘monolayer’ and ~11 nm i.e. ‘multilayer’) prepared using different polymer concentration and solvents (chloroform and toluene) are found to compose of grain-like structures (of size ξ) of predominantly edge-on orientation (probably to maximize the coverage of the low energy methyl groups at both the interfaces) with some defects. Edge-on oriented grains are particularly prominent for the monolayer films (ξ ≈ 50 nm), where the interactions at both the interfaces are weak, but not in the case of the multilayer films (ξ ≈ 10 nm), where out-of-plane interaction between P3DDT molecules and evaporation rate of solvent also become important. Slow evaporation of toluene creates better ordering in that multilayer film. Solvent vapor annealing of the films although reduces the defects, forms small size grains with relatively less ordered structure due to near dissolution (or coil-like conformation) of the P3DDT at saturated vapor of good solvent and subsequent hindrance in the recovery of rod-like conformation and its ϖ-ϖ stacking under fast solvent evaporation. The change in the grain-size is only effective on the monolayer films, where the initial grain-size was large, while the change in the ordering is mainly effective on the toluene evaporated multilayer film, where the initial ordering was better. Further thermal annealing of the films only recovers the size of the grains and the ordering of the P3DDT molecules to a very small extent. However, thermal annealing in presence of solvent vapor on the as-deposited multilayer film show remarkable improvement of edge-on ordering. It is likely that the temperature first restrict the amount of solvent vapor and then such limited vapor pressure in presence of an intermediate temperature helps the reorganization of P3DDT molecules to form edge-on oriented structure.