Creating folders even if already exist or removing removing their content
The second one is definitively safer, since in the first one you actually remove everything in all subfolders of directory, not just in the three folders you want to remove.

Some additional comments:


I would save the result of os.path.join(directory, folder) in a variable, you calculate it like three times.
Have a look at Python's official style-guide, PEP8. It recommends using lower_case both for variables and for function names, so your function should be called clean_folders.
A bare except is basically never a good idea. And even worse is a bare except with the unhelpful message 'something went wrong'. You want to either catch the exception you are looking for and handle it, or let the exception bubble to the top and halt the execution of the program. So, find out what kind of exception you actually want to catch (maybe IOError?). Or at least use except Exception, which excludes exceptions like e.g. the user pressing Ctrl+C being caught.