This study focuses on easing or eliminating potential punch-through in two-layer stiff-over-soft clay deposits by tweaking spudcan shapes. The effectiveness of skirted spudcans with and without holes, relative to a generic spudcan used conventionally, is tested. Three-dimensional large deformation finite element (LDFE) analyses are carried out systematically; encompassing a parametric study on the length of the skirt on the bottom periphery, number of holes through the spudcan base, and the slope of the spudcan base. Numerical results lead to selection of two skirted spudcans with and without holes, and both with a skirt length of ∼0.23 spudcan diameter. The performance of those two spudcans is then tested through a series of centrifuge model tests; varying the strength ratio between the two layers, and the thickness of the stiff layer relative to the spudcan diameter. Overall, the results of eighteen penetration tests suggest that the skirted spudcan without holes is more effective in easing or even eliminating the punch-through that is associated with the penetration of the generic spudcan. For using the skirted spudcan without holes in the field, an improved analytical model is proposed for assessing penetration resistance profile or embedment depth under a given preload.