Kinematic couplings have been used to create palletized system for part transfer in a microfactory. While kinematic couplings provide high repeatability, calibration is needed to achieve high interchangeability accuracy. In this paper, a generalized artifact-based methodology for pallet calibration and workpiece registration is developed. This calibration method uses the microfactory machines to both machine and measure artifacts to estimate the interchangeability errors. The error sources affecting the accuracy of calibration are analyzed and techniques are suggested to reduce these errors. Finally, the methodology is applied and validated for a specific microfactory application.