Hot tapping is a critical technique for modifying subsea pipeline systems without interrupting operations. It requires seabed interventions (SBI) to ensure stability during excavation, rock infilling, and equipment installation—particularly in soft clay environments with high loads and moments. Finite element analysis (FEA) is commonly used to assess SBI stability, with two-dimensional (2D) models often preferred for their simplicity and speed. However, 2D analyses assume plane strain conditions and may not capture the inherently three-dimensional nature of the problem.This study compares 2D and three-dimensional (3D) FEA using RS2 and RS3 software across various excavation geometries, infill heights, and loading conditions. Results show that 2D models, even when applied in multiple planes, can miss critical failure mechanisms—especially under concentrated loads, large deformations, or in the presence of weak topsoil. While 3D models offer more realistic behaviour and capture complex interactions, they require significantly more setup time and computational effort.Unconverged 3D cases may indicate overlooked risks but must be supported by sensitivity studies to ensure meaningful interpretation. The findings highlight the trade-offs between modelling fidelity and efficiency, supporting more informed decisions in selecting analysis methods for safe and cost-effective SBI design.