A computer-implemented method of generating resection plane and checkpoint positioning data for use with a navigation system in planning an arthroplasty procedure on a patient bone, the computer-implemented method comprising: obtaining patient data associated with at least a portion of the patient bone, the patient data captured using a medical imaging machine; generating a three-dimensional patient bone model (226, 224) from the patient data; identifying a first location of a first checkpoint on the three-dimensional patient bone model (226, 224) via user input; identifying a second location of a resection plane (334, 306) relative to the three-dimensional patient bone model (226, 224) via user input, the resection plane (334, 306) defining a resection surface on the three-dimensional patient bone model (226, 224) to be exposed following a resection; determining a shortest signed distance vector (d) from the first location to a point on the resection surface; using information associated with the shortest signed distance vector (d) to determine if the first location of the first checkpoint is located too close to the second location of the resection plane (334, 306) so as to interfere with or be resected by the resection; if the first location of the first checkpoint is located too close to the second location of the resection plane (334, 306), alerting a user and modifying via user input the first location of the first checkpoint or the second location of the resection plane (334, 306); and generating the resection plane and checkpoint positioning data using information associated with the first location of the first checkpoint and the second location of the resection plane (334, 306). obtaining patient data associated with at least a portion of the patient bone, the patient data captured using a medical imaging machine; generating a three-dimensional patient bone model (226, 224) from the patient data; identifying a first location of a first checkpoint on the three-dimensional patient bone model (226, 224) via user input; identifying a second location of a resection plane (334, 306) relative to the three-dimensional patient bone model (226, 224) via user input, the resection plane (334, 306) defining a resection surface on the three-dimensional patient bone model (226, 224) to be exposed following a resection; determining a shortest signed distance vector (d) from the first location to a point on the resection surface; using information associated with the shortest signed distance vector (d) to determine if the first location of the first checkpoint is located too close to the second location of the resection plane (334, 306) so as to interfere with or be resected by the resection; if the first location of the first checkpoint is located too close to the second location of the resection plane (334, 306), alerting a user and modifying via user input the first location of the first checkpoint or the second location of the resection plane (334, 306); and generating the resection plane and checkpoint positioning data using information associated with the first location of the first checkpoint and the second location of the resection plane (334, 306).