Taken directly from their help file which should have been included with your install
The ease with which Wrye Bash can be removed is dependent on how much you use it to manage your modded game.
If you use a Bashed Patch, you will need to remove any dependencies on it from your saves before uninstalling Wrye Bash in order to avoid in-game issues. This may be near-impossible to do, depending on what is in your Bashed Patch.
If you use BAIN to manage your installed mods, you will need to ensure that you have an adequate alternative management system ready, as although uninstalling Wrye Bash will not uninstall your mods, you will no longer be able to use BAIN's conflict resolution features.
If you use any INI tweaks applied through Wrye Bash, you will need to make a note of which tweaks you have applied, as although uninstalling Wrye Bash will not undo your tweaks, you will no longer have any record of tweaks applied or default values.
If you use the People tab, you will need to transfer your notes on people and record their karma outside of Wrye Bash.
If you use the PM Archive tab, you will need to move your archived PMs outside of Wrye Bash's folders.
If none of the above points apply to you, or once you have taken the necessary measures for the points that apply, you can uninstall Wrye Bash by either running the uninstaller, if you used the installer to install Wrye Bash, or delete the following files and folders if you installed it manually.
[Game]\Mopy - If you've edited any localisation files in the l10n folder that you want to keep, back them up.
[Game]\Data\Bash Patches - If you've exported any CSV files that you want to keep, back them up.
Documents\My Games\[Game] - Only delete the BashProfiles.dat, BashProfiles.dat.bak, BashSettings.dat, BashSettings.dat.bak, Messages.dat, Messages.dat.bak, People.dat and People.dat.bak files and the Saves\Bash folder.
[Game] Mods (in the same folder as [Game]) - The Bash Installers folder stores the mods you've installed via BAIN.