In the last decades, optimizing implant properties in terms of materials and biointerface characteristics represents one of the main quests in biomedical research. Modifying and engineering polyvinylidene fluoride (PVDF) as scaffolds becomes more and more attractive to multiples areas of bio-applications (e.g., bone or cochlear implants). Nevertheless, the acceptance of an implant is affected by its inflammatory potency caused by surface-induced modification. Therefore, in this work, three types of nano-micro squared wells like PVDF structures (i.e., reversed pyramidal shape with depths from 0.8 to 2.5 microns) were obtained by replication, and the influence of their characteristics on the inflammatory response of human macrophages was investigated in vitro. FTIR and X-ray photoelectron spectroscopy analysis confirmed the maintaining chemical structures of the replicated surfaces, while the topographical surface characteristics were evaluated by AFM and SEM analysis. Contact angle and surface energy analysis indicated a modification from superhydrophobicity of casted materials to moderate hydrophobicity based on the structure’s depth change. The effects induced by PVDF casted and micron-sized reversed pyramidal replicas on macrophages behavior were evaluated in normal and inflammatory conditions (lipopolysaccharide treatment) using colorimetric, microscopy, and ELISA methods. Our results demonstrate that the depth of the microstructured surface affects the activity of macrophages and that the modification of topography could influence both the hydrophobicity of the surface and the inflammatory response.