How to solidify a complex 2D Render from Pix4D for 3D printing I have looked everywhere but cannot find exactly what i need help with so hopefully someone can help me. 

I currently have this file 

As you can see it is a 2D mesh generated out of a program called Pix4D Mapper.

I would like to make it a solid single 3D model so that i may print it via a 3D printer. To do this i would like to fill in the area inside of the blue box so that it is solid. 

Is there a simple tool to do this? Right now i have been creating a flat version of the file below and then linking the edges of the top and bottom one with new faces however this will take upwards of 7 hours for the whole file and may not even work. The problem is that there are different elevations on the work site that we scanned and without filling in the area we cannot 3D print the file.

I already tried using the solidify tool but due the complexity of the model it ruins the buildings and levies when solidifying it. Is there any other way to do this? 

Also is there anything else that should be done before printing?
If I get how your model is done now, I would select the outer edge, and then extrude it down Z enough.  Then Scale it to Z 0 (zero) to equal the bottom extruded edge loop. Then fill the bottom face pressing F key.