The evaluation of non-aligned multiple cracks is required in various fitness-for-service codes. For non-aligned parallel cracks, on-site inspection needs to decide whether the cracks should be treated as coalesced or separate multiple cracks for Fitness-for-Service. In the existing literature, criteria and standards for the adjustment of multiple nonaligned cracks are very source dependent, and those criteria and standards are often derived from on-site service experience without rigorous and systematic verification. Based on this observation, the authors previously reported on the effect between an edge and an embedded parallel crack in 2-D scenarios and, more recently, in 3-D scenarios of circular cracks. Since realistic crack configurations detected using non-destructive methods are generally 3-D in nature, the study of 3-D effect of non-aligned cracks with different shapes is deemed necessary in order to obtain more practical guidance in the usage of rules speculated in Fitness-for-Service codes. In this study, a quarter-circle corner crack is considered to interact with a semi-elliptic non-aligned surface flaw in an infinitely large plate under uniaxial tension. While keeping the geometry of the quarter-circle corner crack unchanged, a pair of horizontal (H) and vertical (S) separation distances between the two cracks is chosen followed by a detailed analysis of the effect of crack shape on the 3D SIFs for various embedded semi-elliptical cracks. The analysis is repeated for various combinations of separation distances S and H. The results from this study are collectively significant to the understanding of the correlation between the criteria and standards in Fitness-for-Service community and the consequence of their usage in engineering practice.