This project explores the potential for 3D modelling and printing to create customised flutes that can play music in a variety of microtonal scales. One of the challenges in the field of microtonality is that conventional musical instruments are inadequate for realising the abundance of theoretical tunings that musicians wish to investigate. This paper focuses on the development of two types of flutes, the recorder and transverse flute, with interchangeable mouthpieces. These flutes are designed to play subharmonic microtonal scales. The discussion provides an overview of the design and implementation process, including calculation methods for acoustic modelling and 3D printing technologies, as well as an evaluation of some of the difficulties encountered. Results from our 3D printed flutes suggest that whilst further refinements are necessary in our designs, 3D modelling and printing techniques offer new and valuable methods for the design and production of customised musical instruments. The long term goal of this project is to create a system in which users can specify the tuning of their instrument to generate a 3D model and have it printed on demand.