The field of Neuro-Engineering seems to be on the fast track towards accomplishing its ultimate goal of potentially replacing the nervous system in the face of disease. Meanwhile, the patients and professionals involved are continuously dealing with human bodily experience and especially how neuro-engineering devices could become part of a user’s body schema: the domain of ‘embodied phenomenology’. This focus on embodiment, however, is not sufficiently reflected in the current literature on ethical and philosophical issues in neuro-engineering. In this article we will focus on this lacuna by explaining existing data on neuro-engineering user’s experiences by using phenomenological concepts such as transparency and the concepts that may facilitate this: functionality, sensorimotor feedback and affective tolerance. By introducing and applying these concepts to four real life case examples, we will discuss practical implications and guidelines which can contribute to the actual success of incorporation of the device by the patient. First, we will discuss the importance of a ‘Patient Preference Diagnosis’, which can serve as a way to prepare the patient for the existential reorientation involved in the process. In addition, a Patient Transparency Diagnosis during and after such a process is also relevant when wanting to provide the medical field in general with feedback, and the patient in particular with possibilities to fine-tune the device. From these practical guidelines we will conclude that the phenomenological approach can be very valuable when applied to the field of neuro-engineering.