A computer-implemented method for fully-autonomous level identification of anatomical structures within a three-dimensional medical imagery, includes: receiving a set of medical scan images of the anatomical structures; processing the set to perform an autonomous semantic segmentation of anatomical components and to store segmentation results; processing segmentation results by removing the false positives, and smoothing 3D surfaces of the generated anatomical components; determining morphological and spatial relationships of the anatomical components; grouping the anatomical components to form separate levels based on the morphological and spatial relationships of the anatomical components; processing the set using a convolutional neural network to autonomously assign an initial level type; assigning the determined level type to each group of anatomical components by combining the determined morphological and spatial relationships with the determined initial level type; assigning an ordinal identifier to each group of anatomical components; and storing information about the assigned levels with their ordinal identifier.