A bone cutting jig system for forming and shaping spinal implants is shown. The system includes a first cutting jig having a bed with a clamp mechanism for clamping donor bone positioned on the bed. A cutting guide insert or plate is received in fixed orientation on the bed and is further provided with two spaced cutting blade cutting guides which are configured for transversely cutting out a segment of the donor bone with a reciprocating saw or router to a predetermined shape to provide a custom fit lumbar, cervical or thoracic inter-body fusion implant. A second cutting jig is provided for making additional cuts to the preformed implant for custom fit to particular implant applications.