1. An integrated surgical system, comprising: a scanning device configured to scan a selected portion of a patient's body and to generate a plurality of two-dimensional images of the selected portion; a surgical machining system comprising a machine tool and means for selectively moving the machine tool relative to a plurality of axes; and a processor operatively connected to the scanning device and the surgical machining system, the processor configured to: receive two-dimensional images from the scanning device; generate a three-dimensional image of the selected portion of the patient's body from the received two-dimensional images, display the three-dimensional image, receive input from the user, the input indicating a location of the selected portion to be machined during surgery and at least one machining property, generate an optimized tool path based at least in part on the input and at least in part on geometry of the three-dimensional image of the selected portion of the patient's body, and transmit the optimized tool path to the surgical machining system to effect movement of the machine tool in accordance with the optimized tool path in an automated manner; wherein the processor is configured to update the optimized tool path based on detected differences between actual properties of the selected portion of the patient's body and expected properties of the three-dimensional image of the selected portion.