We have fabricated poly(ε-caprolactone) (PCL) films with flat and honeycomb-patterned (HCP) structures to coat polyaniline (PANI) on the film surface. In addition, the effect of chemical modification of PANI by sulfuric acid (H2SO4) was also studied for antibacterial activity. The flat and HCP PCL films were obtained by simple evaporation of the solvent and via the breath figure (BF) method, respectively. The morphology and chemical composition of PANI coated on the film surface were evaluated by scanning electron microscopy (SEM) and X-ray spectroscopy (EDX). Fourier transform infrared spectroscopy (FT-IR) and thermogravimetric analyses (TGA) were obtained to identify the PANI coating. The wettability and conductivity of the films were also measured. Applicational aspects were evaluated by assessing antibacterial and antibiofilm activity against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus). The EDX, TGA, and FT-IR findings indicated chemical modification of PCL film by PANI and H2SO4. The conductivity of the films was increased by the coating of PANI to the patterned surface and additionally increased by the chemically modified PANI. The antibacterial activity was 69.79%, 78.27%, and 88% against E. coli, and 32.73%, 62.65%, and 87.97% against S. aureus, for flat PANI, HCP PANI, and H2SO4-treated HCP films, respectively. Likewise, the PANI coated flat, HCP, and H2SO4-treated HCP films inhibited E. coli biofilm formation by around 41.62%, 63%, and 83.88% and S. aureus biofilm formation by 17.81%, 69.83%, and 96.57%, respectively. The antibacterial activity of the HCP film was higher than that of flat PANI films, probably due to the higher coating of PANI on the HCP surface. Moreover, sulfonation of the HCP film with H2SO4 might have improved the wettability, thereby enhancing the antibacterial and antibiofilm properties. Our results showed that topographical changes, as well as doping, offer simple and cost-effective ways to modify the structural and functional properties of films.