Embodiments of the present disclosure are directed to methods and computer systems for converting datasets into three-dimensional (“3D”) mesh surface visualization, displaying the mesh surface on a computer display, comparing two three-dimensional mesh surface structures by blending two primary different primary colors to create a secondary color, and computing the distance between two three-dimensional mesh surface structures converted from two closely-matched datasets. For qualitative analysis, the system includes a three-dimensional structure comparison control engine that is configured to convert dataset with three-dimensional structure into three-dimensional surfaces with mesh surface visualization. The control engine is also configured to assign color and translucency value to the three-dimensional surface for the user to do qualitative comparison analysis. For quantitative analysis, the control engine is configured to compute the distance field between two closely-matched datasets.