The fast-growing technology of additive manufacturing(AM), 3D printing, enables unique features in numerous design areas including musical instrument design. The recent advancements further introduce incorporating electronics into 3D printing. While still in the proof of concept phase, the ability to fabricate embedded sensors with 3D printing offers promising applications for musical instrument design. In this paper, embedding sensors and functional parts in the additive manufacturing process is discussed. We present the design process of embedded sensing for rapid prototyping digital musical instruments (DMI). The establishment of 3D models and operation sequences for different musical applications can be challenging since they vary depending on the electronic components. In order to address this problem, we provide a set of design and manufacturing specifications to customize the prototyping process for embedding structural electronics. The application of this hybrid method is demonstrated with two case studies: modular structures for a wearable gestural controller and an augmented flute. These instruments present the current stage of the technology which uses fused-deposition modeling (FDM) and the advantages and challenges of hybrid AM in musical instrument design as well as its future directions.