The soil structure interaction is an eternal issue that may affect the actual behavior and design of the structures. For many years the civil engineers are dealing with this issue as an important issue and should be investigated. In this study, the conventional finite element method is adopted. Also, the effects of some important analytical modeling parameters on the dynamic response of structures under horizontal and vertical ground motions are taken into considerations. Structural type, aspect ratio, the soil mass, dimension of soil model, and boundary conditions are important effects on design and analysis of soil structure interaction, therefore, this study focuses on these effects. The structural system in this study consist of 5,10,15 stories moment resisting frame and concentrically braced frame. Aspect ratios of (height: base) 1:2, 1:1, 2:1 are adopted with story height of 3 meters. Under all structures, a continuous reinforced concrete foundation is assumed. The soil- structure system also has a soil media with a constant depth of 80 meters. Two general methods of soil structure analysis are used in research. The first one is the sub-structure method which is defined by using an artificial border immediately under the base of the structural foundation and the concept of dynamic impedance of the unbounded soil media. The second one is a direct method which is directly part of the unbounded soil media. Using direct method seems more appropriate with finite element software. Iranian seismic code (Standard 2800, BHRC, 2005) is used assuming a fixed base, soil type III and maximum ground acceleration of 0.35g and designed according to part 10 of national building regulations (INRB, 2008). Also, Soil has shear wave velocity of 300 m/s, deformation modulus of E = 466 N/mm2, poison ratio v = 0.35, and density of 18 KN/m3. Sap2000 program is used for finite element modeling of the soil-structure problem. Two dimensions plane strain elastic elements are used for modeling and two alternatives of soil modeling are selected. The first alternative (mass) which includes the mass of soil. The second alternative (massless) does not include the mass of soil. Nonlinear GAP connector elements are used between the reinforced concrete foundation of the structure and the soil in order to complete the soil structure construction of the soil-structure model. GAP connectors consist of an elastic spring and an incorporated opening so that no tensile forces are transmitted between the structure and the soil. The behavior of GAP element is linear elastic under compressive forces. The GAP elements are put in every-one meter along the length of the structural foundation with high spring stiffness value (104 KN/m). The damping is assumed as 4% of the critical damping using Rayleigh damping definition. The boundary conditions for the analytical model are represented for horizontal and vertical soil boundaries. For horizontal soil boundaries, a fixed boundary is assumed at the base of the soil model. But, for vertical soil boundaries, three alternatives are assumed. First free boundary, within these boundaries the displacement at the side boundaries are free from any constraints and take place vertically. Second tied boundaries, in these boundaries the corresponding nodes on two vertical boundaries at two sides of the soil model are tied to each other thus their horizontal and vertical displacement are the same all times during the analysis. Third transmitting boundaries, these boundaries are presented by viscous dampers at the boundaries. These dampers can absorb body waves propagation to the boundary. Three ground motions with horizontal and vertical components are selected for dynamic analysis. Selection depends on soil type and seismic hazard scenario considered in the design of the structures. The selected ground motions are Cape Mendocino, Duzce Turkey, and Loma Prieta. These ground motions are applied to the fixed base of the soil model. All responses are considered in terms of maximum base shear and interstory drifts. Further, responses are compared to each other in different models as well as the models without soil-structure interaction. It has been noticed that the soil model does not have an effect on the propagation of waves, thereby, for massless soil models the free ground motions are directly applied. Also, for the free field response, it is noticed that the model with tied boundary conditions performs well in simulating the free field motion both at the near and far point of soil system and under both horizontal and vertical component of the earthquake. Soil domain size does not have any effects on the base shear value for different structures. When the structure is present on the soil layer the ground motion characteristics near to the structure and the extent of the modifications change due to the structure height (period), and type of the structure and earthquake. The type of boundary modeling directly affects the seismic response of different structural models. Moreover, it is noticed that the increase of the height of the structure is also increasing the seismic response of different structures models which have different boundary types. But for the small structures, the response values are closed to each other. The dynamic SSI may affect the seismic responses depending on the characteristics of the soil and structure. Also, taking SSI into consideration increases the drift values especially in tall structures. In addition, tied boundary modeling has clear performance better than free and transmitted boundaries. Finally, the researchers suggested that this study needs more accurate modeling by using available more advanced analytical tools.