This article presents application of modal analysis for the computation of biometric data base (3D faces) and extraction of three dimensional geometrical features. Traditional anthropometric database contains information only about some characteristic points recorded as linear or angular dimensions. The current face recognition systems are also based on the two-dimensional information. To increase level of security the methods need to operate on threedimensional data. In the article authors present of 3D modal analysis, for decomposition, extraction features and individual coding of analyzed objects sets. Authors apply empirical modal analysis PCA (Principal Component Analysis) for 3D data of human faces. Additionally for face recognition, the comparison of reconstruction with different number of modes are presented and discussed.