A method and system of volume deformation, including accessing a tree structure for a set of deformation maps. The tree structure is traversed for each voxel in an original volume and each voxel is transformed according to each deformation map corresponding to a node of the tree structure until the entire original volume is deformed into reference volume space. Also, a method and system of generating an ordered map tree structure, including identifying a root node of a bounding box, the bounding box being a union of the root node's descendants. Child nodes are identified for each node, the child nodes being ordered so that a left child is applied before a corresponding right child, wherein each child node contains a deformation map and a corresponding bounding box. Each path originating from the root node corresponds to a complete deformation map sequence, and when a portion of two deformation maps overlap, the deformation map having a lower priority is a child of the deformation map having a higher priority.