Ok I can see what your planning to do a little better now. I agree with the above. A DEM for the base is probably the easiest. Now if the resolution of the final image is quite low then you could raise up the buildings as part of the DEM. But its better if you use a vector app for the buildings. The QGIS plugin sounds like a good idea. Also, inkscape can trace out a bitmap into vector format and then usually you can import those vector traces into something like blender to make them into a 3D model. You should also check out sketchup which is particularly suited to this kind of buildings on a 3D base kind of work tho I have not used that one much. If its important for you to maintain the georefferencing then a GIS app is probably a must. Global Mapper has been used on here with some good success as well as QGIS. ArcGIS is the professional app but its very expensive and I think for what you wish to do its probably over kill unless you have a copy you can use.