Repair of technological defects and operational damages identified during technical control in manufacture process and preventive inspection in operation is required element of the organizational and technical system for ensuring the operational robustness of aircraft structures. An analysis of various types of repairs shows that despite a rather low efficiency, mechanical (i.e. riveted and bolted) joints have the lowest labor input that promotes their application at operation of the aircraft equipment. For verification calculation of the panels with cutouts repaired mechanically, numerical methods for strength calculation using two-dimensional and three-dimensional modeling are justified. In two-dimensional modeling, a thin-walled structure is generated from flat quadrangular or triangular elements, the size of which should be approximately equal the diameter of the fastening bolts connecting the separate structural elements. Fasteners (rivets or bolts) in two-dimensional modeling of the panel were replaced by springs, and in three-dimensional modeling, they were generated from solid elements. Formulas were used that widely applied in designing by foreign aviation companies to simulate the flexibility of fasteners for single-shear joint. In three-dimensional modeling of joints, both the panel and the cover plate are generated from prisms with four, eight or more tops. Fasteners are also developed by solid elements. In this case, the contact problem of the interaction between the fastener elements and the panel parts is solved. The modified Nuizmer criterion is used previously developed to evaluate the strength of composite plates with cutouts to estimate the load bearing of the panel with repaired cutout. The calculation reliability is checked by comparison with experimental data obtained during the testing of full-scale composite panels.