Understanding the defect removal process is crucial for fabricating defect-free self-assembled structures in block copolymer thin films. Most previous studies mainly focused on the removal of in-plane dislocation and disclination defects, while out-of-plane defects receive less attention. In this study, the removal of two types of out-of-plane defects of lamellar forming block copolymer thin films, the tilted domain defect and the cross-sectional edge dislocation defect, are studied in detail using the string method coupled with the numerical self-consistent field theory (SCFT). It is found that the removal of the tilted domain defect can be regarded as an order-order transition process controlled by the nucleation and growth mechanism. On the other hand, the cross-sectional edge dislocation can be eliminated by either evaporating or growing its core (a partial domain). For both cases, multiple removal pathways have been identified by varying the height of the partial domains and the segregation strength of the block copolymer. Phase-diagram-like maps are constructed to show which removal pathway can occur most probably at given height and segregation strength. In the strong segregation regime, in consistent with that found in the removal of in-plane defects, one or more "bridge" structures are formed, which serve as a channel for diffusion of polymer chains. When the segregation is weak, however, no actual bridge but only a nascent bridge structure, whose density of A components in the B domain is slightly higher than the averaging value, is observed and plays a similar role as the actual bridge.