Various researchers have contributed to the identification of the mass and stiffness matrices of two dimensional (2-D) shear building structural models for a given set of vibratory frequencies. The suggested methods are based on the specific characteristics of the Jacobi matrices, i.e., symmetric, tri-diagonal and semi-positive definite matrices. However, in case of three dimensional (3-D) structural models, those methods are no longer applicable, since their stiffness matrices are not tri-diagonal. In this paper the inverse problem for a special class of vibratory structural systems, i.e., 3-D shear building models, is investigated. A practical algorithm is proposed for solving the inverse eigenvalue problem for un-damped, 3-D shear buildings. The problem is addressed in two steps. First, using the target frequencies, a so-called normalized eigenvector matrix, which is a banded matrix containing the information related to the frequencies and mode shapes of the target structural system, is determined. In this regard, similar to the solution of inverse problem for 2-D shear building structural models in which an auxiliary structure is constructed by adding constraints (or springs) to the original system, three auxiliary structures are proposed to solve the problem for 3-D cases. In the second step, the normalized eigenvector matrix is utilized to obtain the normalized stiffness matrix; in turn, this matrix is decomposed into the stiffness and mass matrices of the system. Finally, a numerical example is presented to demonstrate the efficiency of the proposed algorithm in determining the mass and stiffness matrices of a 3-D structural model for a given set of target vibrational frequencies.