This will be your unmodified game, (also called vanilla) with the official patch already installed (if you installed it already) back to the exact configuration it was in before you installed any mods. It will not affect OBSE as that is installed in the Oblivion folder. It Will remove any OBSE plug ins though. This will not remove your saved games.
Order Must Be Restored Vanilla
Guide to removing all 3rd-party mods and other files from your Skyrim installation - by, wikified by Farlo. The best way of course is to use your zip file that you made of the Skyrim Directory as you followed the, just delete the whole directory and unpack the zip.