The only thing you can do is uninstall them one by one. Deleting the mods in the folder may cause NMM to crash.
Deleting the original mod files won't remove them from the game, but it will prevent NMM from ever uninstalling them (you'd have to go in and manually delete the files, assuming you could find out which files they were).
Beside that you should start a new character after that, because your save(s) relies on those mod's.
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If you delete your data folder, you should verify your game cache files and install them again via steam, and should get you back to vanilla.!!!!!!
But - Some mods replace the default textures in the skyrim data folder. If you delete them, the game will run ( or won't run at all ) without any textures, and you don't want that. Typically it's good practice to make a copy of the default textures and meshes folders. If you didn't do that, there really is no way as far as I know to replace the modded textures with the default ones. So short answer, no you do not just delete the folders; yes you should reinstall.
I am not very familiar with NMM, but this guide shows you how you manage your files with NMM: http://hubpages.com/hub/How-to-use-Nexus-Mod-Manager-to-download-install-uninstall-and-manage-Skyrim-Oblivion-Morrowind-and-Witcher-2-mods