Robotic systems and methods for robotic arthroplasty. The robotic system includes a machining station and a guidance station. The guidance station tracks movement of various objects in the operating room, such as a surgical tool, a humerus of a patient, and a scapula of the patient. The guidance station tracks these objects for purposes of controlling movement of the surgical tool relative to virtual cutting boundaries or other virtual objects associated with the humerus and scapula to facilitate preparation of bone to receive a shoulder implant system. The virtual objects are located based on density data of the bone such that, when one or more shoulder implants are fully seated in the bone, distal portions of the implants are located in a first region of the bone having a density characteristic greater than an adjacent second region of the bone.