A novel design method has recently been proposed for the seismic protection of structures on liquefied ground using shallow (instead of deep) foundations. Contrary to conventional structural isolation approaches, which employ special mechanical devices, the proposed geotechnical means exploits the presence of natural liquefiable soil, after partial remediation of the surface ground, as a natural base isolation system which de-amplifies the seismic ground motion and, hence, reduces the seismic demand on the superstructure. This paper focuses on the comparative evaluation of the relevant Soil-Foundation-Structure Interaction (SFSI) effects. Using an equivalent-linear approach based on appropriate values for the material properties of liquefied soil, the dynamic stiffness and damping of rigid square footings on three-layer liquefiable soil under external harmonic oscillations is first numerically investigated. Results demonstrate that for common soil, foundation and seismic excitation conditions, liquefaction leads to (a) significant reduction in dynamic stiffness and (b) increase in damping of the footing over pre-liquefied conditions. Based on these results, regression formulae for estimating static stiffness of surface footings on liquefied soil were developed. In the second part of the paper, parametric numerical analyses are presented for the typical case of bridge piers on liquefiable soil, with surface foundation and a remediated surface crust. Results from both harmonic steady-state and transient analyses indicate that the effect of soil liquefaction on the vibrational characteristics of the pier-foundation system decreases drastically with increasing soil crust thickness and, consequently, the intended natural base isolation of the structural system is mainly achieved by the reduction in free-field seismic ground response.