One embodiment of the present invention provides a system for masking index values in a database. During operation, the system receives a request to mask a column in a database, wherein the column is an index-column. Next, the system retrieves a tree which is used to index the column, wherein the tree provides a sorted representation of values in the column. The system then locates the root-node of the tree. Then, for each child-node in the tree, the system determines if the child-node is a leaf-node. If so, the system masks a node-value for the leaf-node without resorting the tree. If not, the system leaves the node-value unmasked.