In VS2013, after you have setup the "publish" (right click on the website and choose Publish Web Site), a new configuration file (website.publishproj) will be added to the project.
To exclude the folders, you have to open this file and add the following section with the "project" section:
<ItemGroup>
<ExcludeFromPackageFolders Include="log;temp;">
<FromTarget>Remove temp folders</FromTarget>
</ExcludeFromPackageFolders>
</ItemGroup>
In the "Include" attribute, it contains the folder to be removed when publishing the website. The above example excluding "log" and "temp" folders.
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