The ability to control thin-film growth has led to advances in our understanding of fundamental physics as well as to the emergence of novel technologies. However, common thin-film growth techniques introduce a number of limitations related to the concentration of defects on film interfaces and surfaces that limit the scope of systems that can be produced and studied experimentally. Here, we developed an ion-beam based subtractive fabrication process that enables creation and modification of thin films with pre-defined thicknesses. To accomplish this we transformed a multimodal imaging platform that combines time-of-flight secondary ion mass spectrometry with atomic force microscopy to a unique fabrication tool that allows for precise sputtering of the nanometer-thin layers of material. To demonstrate fabrication of thin-films with in situ feedback and control on film thickness and functionality we systematically studied thickness dependence of ferroelectric switching of lead-zirconate-titanate, within a single epitaxial film. Our results demonstrate that through a subtractive film fabrication process we can control the piezoelectric response as a function of film thickness as well as improve on the overall piezoelectric response versus an untreated film.