A simulation-based approach to the design of procedure-specific dexterous neuroendoscopic continuum instruments for endoscopic third ventriculostomy and tumor biopsy is proposed. Given pre-operative CT and MRI images, the algorithm returns instrument design specifications including lengths, curvatures and alternative positions for the surgical incision while respecting anatomical boundaries. This methodology proposes a novel clinically-guided geometric representation of surgical targets specific to this indication. The additional constraints imposed by the presence of surgical trocars and endoscopes are also considered. Finally, we conclude with a clinical example to demonstrate the proposed approach.