A burr hole plug comprises a plug base configured for being mounted around a burr hole. The plug base includes an aperture through which an elongated medical device exiting the burr hole may pass. The plug base is configured to accommodate a variety of cranium forms without requiring deformation of the plug base. A plug base holding tool is used to secure the plug base to the cranium, wherein the tool aligns fasteners with the plug base for insertion through the plug base and into the cranium. The burr hole plug further comprises a retainer configured for being mounted within the aperture of the plug base to secure the medical device. The retainer includes a clamping mechanism that secures the elongated medical device in the burr hole plug, wherein the movement of the clamping mechanism is controlled to prevent skewing of the clamping mechanism.