I need to know for example, heights of bridges/fly-overs from the land surface (just to know there is an elevated structure). How and where from can I get this data (preferably for EU)? Any open source databases/ any 3d maps with this data?
There appears to be a US government program to map structural heights, suggesting that such a thing isn't already available. Quoting http://nationalmap.gov/3DEP/
The 3D Elevation Program (3DEP) initiative is being developed to respond to growing needs for high-quality topographic data and for a wide range of other three-dimensional representations of the Nation's natural and constructed features.
You can find existing elevation data at:
or by clicking on the "Get Elevation Data" link at http://nationalmap.gov/elevation.html
The maps here are 1/9 arcsecond per pixel, which is right about 10 feet per pixel in latitude.
http://nationalmap.gov/3DEP/3dep_prodavailability.html notes that you can get 1m (about 3 feet) resolution digital elevation maps; however, it appears that this data isn't available online and that you must make a special request for it.
Of course, you're looking more for EU data. The US government does have some of this too: https://lta.cr.usgs.gov/elevation.html and http://hydrosheds.cr.usgs.gov/data.php but it seems even the best such data is 3 arcseconds, or about 90 feet per pixel, which might be enough to miss structures.