A prototype process of a physical user interface includes not only connection of electronic parts and an enclosure design, but also the arrangement and configuration of the electronic parts in the enclosure. This process is complicated and difficult for people who do not have modeling skills. We propose ProtoHole, a system for prototyping interactive 3D printed objects using holes, internal cavity and swept-frequency acoustic sensing. By emitting a high-frequency sweep signal inside the object, our system enables to classify changes in resonance properties when closing holes using a machine learning technique. Therefore, an object can be easily made interactive without considering an arrangement of internal electronic parts and wiring. We show examples of prototypes created with our system.