The technology relates to generating a three-dimensional point cloud model of an anatomical structure. A computer accessible memory stores a three-dimensional array of data elements describing multiple anatomical features of a subject, each of the data elements having associated therewith positional data and a separate parameter value. A processor may be configured to identify any data elements in the three-dimensional array having an associated parameter value satisfying a predefined threshold value associated with at least one anatomical feature. The processor may be further configured to generate a visually displayable three-dimensional point cloud model of at least one anatomical structure having a first plurality of points in the point cloud model which define an exterior perimeter of the at least one anatomical structure and a second plurality points in the point cloud model which define at least one feature interior of the exterior perimeter of the at least one anatomical structure.