Automating bone micro-milling using a robotic system presents challenges due to the uncertainties in both the external and internal features of bone tissue. For example, during a mouse cranial window creation, a circular path with a radius of 2 to 4 mm needs to be milled on the mouse skull using a microdrill. The uneven surface and non-uniform thickness of the mouse skull make it difficult to fully automate this process, requiring the system to possess advanced perceptual and adaptive capabilities. In this study, we propose an automatic calibration and 3D surface fitting method and integrate it into an autonomous robotic bone micro-milling system, enabling it to quickly, in real-time, and accurately perceive and adapt to the uneven surface and non-uniform thickness of the target without human assistance. Validation experiments on euthanized mice demonstrate that the improved system achieves a success rate of 85.7 % and an average milling time of 2.1 minutes, showing not only significant performance improvements over the previous system but also exceptional accuracy, speed, and stability compared to human operators.