The real-world measurement of minimum foot clearance (mFC) during the swing phase of gait is critical in efforts to understand and reduce the risk of trip-and-fall incidents in populations with gait impairments. Past research has focused on measuring clearance of a single point on a person's foot, typically the toe-however, this may overestimate mFC and may even be the wrong region of the foot in cases of gait impairments or interventions. In this work, we present a novel method to reconstruct the swing-phase trajectory of an arbitrary number of points on a person's shoe and estimate the instantaneous height and location of whole-foot mFC. This is achieved using a single foot-mounted inertial sensor and personalized shoe geometry scan, assuming a rigid-body IMU-shoe system. This combination allows collection and analysis using out-of-lab tests, potentially including clinical environments. Validation of single marker location using the proposed method vs. motion capture showed height errors with bias less than 0.05 mm, and 95% confidence interval of - 8.18 to + 8.09 mm. The method is demonstrated in an example data set comparing different interventions for foot drop, and it shows clear differences among no intervention, functional electrical stimulation, and ankle-foot orthosis conditions. This method offers researchers and clinicians a rich understanding of a person's gait by providing objective 3D foot kinematics and allowing a unique opportunity to view the regions of the foot where minimum clearance occurs. This information can contribute to a more informed recommendation of specific interventions or assistive technology than is currently possible in standard clinical practice.