I don't think a fresh install of FO3 and NV is required. A friend of mine just installed it on his existing FONV game that had a lot of mods on it and it ran with no issues. .... Come to think of it, I had a lot of mods on my FONV and it ran fine for me as well...
If for some reason you do have to do a fresh install - and if you got it through, or registered it with steam - you can move the data directories and then have steam check the games cache. It will download a new data directory and all will be as it was initially.