A system and method for developing customized apparatus, such as guides, for use in one or more surgical procedures is disclosed. The system and method incorporates a patient's unique anatomical features or morphology, which may be derived from capturing MRI data or CT data, to fabricate at least one custom apparatus or guide. According to a preferred embodiment, the customized apparatus comprises at least one patient-specific surface and or contour, which may be derived from MRI or CT data. Apparatus may be matched in duplicate and oriented around the patient's own anatomy, and may further provide any desired axial alignments or insertional trajectories. In an alternate embodiment, the apparatus may further be aligned and/or matched with at least one other apparatus during the surgical procedure.