There are many solutions to this, and your pick would depend on many factors, like your budget, compability with your existing systems/formats and required functionality. I'll give a few pointers:
For a simple and relatively affordable solution, take a look at SketchUp from Trimble. If this is not up for the job, there are two directions:
From the GIS world we have solutions like ESRI's CityEngine that ties he 3D into any existing GIS systems and formats that would be worth a look.
The CAD world have solutions based on CAD formats and Building information models (BIM) that can be worth a check, like Autodesk's AutoCAD Map 3D/Civil 3D, as seen e.g. in this example from Ordnance Survey in the UK.
There are many other solutions like these that I am not familiar with. A search for CityGML compatible software should give a few alternatives to check out...