Accurately capturing the bone and cartilage morphology and generating a mesh remains a critical step in the workflow of computational knee joint modeling. Currently, there is no standardized method to compare meshes of different element types and nodal densities, making comparisons across research teams a significant challenge. The aim of this paper is to describe a method to quantify differences in knee joint bone and cartilages meshes, independent of bone and cartilage mesh topology. Bone mesh-to-mesh distances, subchondral bone boundaries, and cartilage thicknesses from meshes of any type of mesh are obtained using a series of steps involving registration, resampling, and radial basis function fitting after which the comparisons are performed. Subchondral bone boundaries and cartilage thicknesses are calculated and visualized in a common frame of reference for comparison. The established method is applied to models developed by five modeling teams. Our approach to obtain bone mesh-to-mesh distances decreased the divergence seen in selecting a reference mesh (i.e., comparing mesh A-to-B versus mesh B-to-A). In general, the bone morphology was similar across teams. The cartilage thicknesses for all models were calculated and the mean absolute cartilage thickness difference was presented, the articulating areas had the best agreement across teams. The teams showed disagreement on the subchondral bone boundaries. The method presented in this paper allows for objective comparisons of bone and cartilage geometry that is agnostic to mesh type and nodal density.