The study deals with the physical modeling of a typical building frame resting on pile foundation and embedded in cohesive soil mass using complete three-dimensional finite element analysis. Two different pile groups comprising four piles ($2{ imes}2$) and nine piles ($3{ imes}3$) are considered. Further, three different pile diameters along with the various pile spacings are considered. The elements of the superstructure frame and those of the pile foundation are descretized using twenty-node isoparametric continuum elements. The interface between the pile and pile cap is idealized using sixteen-node isoparametric surface elements. The current study is an improved version of finite element modeling for the soil elements compared to the one reported in the literature (Chore and Ingle 2008). The soil elements are discretized using eight-, nine- and twelve-node continuum elements. Both the elements of superstructure and substructure (i.e., foundation) including soil are assumed to remain in the elastic state at all the time. The interaction analysis is carried out using sub-structure approach in the parametric study. The total stress analysis is carried out considering the immediate behaviour of the soil. The effect of various parameters of the pile foundation such as spacing in a group and number piles in a group, along with pile diameter, is evaluated on the response of superstructure. The response includes the displacement at the top of the frame and bending moment in columns. The soil-structure interaction effect is found to increase displacement in the range of 58-152% and increase the absolute maximum positive and negative moments in the column in the range of 14-15% and 26-28%, respectively. The effect of the soil- structure interaction is observed to be significant for the configuration of the pile groups and the soil considered in the present study.