This research presents new methods for increasing the customization of the surface characteristics of rapid machined patient-specific bone implants. A bone implant is a medical device that is used for replacing missing or damaged bone tissue in a patient's body. It is possible for a bone implant to have three different types of surfaces (articular, periosteal, fracture) which each require different surface characteristics to help provide biocompatibility. It is also desirable to manufacture implants that are customized specifically for an individual patient to increase the stability and fit of the implant, which has been shown to improve patient healing. A research project at Iowa State University involves developing methods for manufacturing implants using a subtractive rapid manufacturing process called CNC-RP, which combines the automated process planning of rapid prototyping (RP) technologies with the capabilities of 4-axis CNC machining. New methods are proposed for providing more effective setup planning for the CNC-RP process, and for isolating the individual surfaces from one another during machining with the goal of increasing customization while preserving biocompatibility of the implant. The methods were used for performing setup planning for machining a bone implant using a surrogate bone material. It was shown that the methods were effective at increasing the customization of the implant, showing a notable increase in the ability to customize the fracture surface.