Seismic risk assessment on a regional scale requires an estimation of ground motion intensity and its spatial variation over large geographical areas. This task is particularly challenging in the presence of very soft soil deposits where significant amplification occurs at specific frequencies that are often referred to as local resonances. It is often not feasible to conduct a nonlinear site response analysis at thousands of sites of interest across a region such as an urban area due to the computational effort involved and the required detailed information on soil profiles at each site. Thus, in regional seismic risk analyses the hazard is typically represented by a field of response spectral ordinates estimated by ground motion models. This study proposes a simplified site response analysis procedure to improve the characterization of spectral ordinates to be used in regional seismic risk assessments. In the proposed procedure, reduced-order models are used to conduct site response analysis using very few parameters to transform response spectra at rock outcrop into response spectra at the surface of each of the sites. A particular emphasis is given to soft-soil sites characterized by low shear-wave velocities overlaid on rock or firm soils. A non-uniform continuous shear beam model with a parabolic variation of shear modulus along the depth and modal damping is used in combination with Random Vibration Theory. It is shown that the proposed approach provides better estimates than those of ground motion models or physics-based ground motion simulation models which often cannot capture the local resonances. Site-specific validation of the shear beam model and overall simplified site response analysis is performed at four soft-soil sites in San Francisco, California. Despite its simplicity, it is shown that the proposed procedure adequately captures the amplitudes and spectral shapes of the motions. It is also shown that in conjunction with ground motion models or physics-based models, the proposed simplified site response analysis procedure can be used to efficiently simulate the seismic hazard on a regional scale through an example of a regional seismic hazard analysis of 160 softer soil sites in Downtown San Francisco during the Loma Prieta earthquake.