I don't like AucTeX very much yet, but I'm trying. Here are things I've "found out".
AucTeX provides a simple interface to clean the files. Hitting C-c C-c and typing 'Clean' or 'Clean All' deletes the intermediate files associated with the current .tex in the buffer.
That's right, it ONLY deletes the intermediate files with respect to the current buffer where C-c C-c is called.
The difference between 'Clean' and 'Clean All' is that, in the latter case, the output files are also deleted. And the files can also be deleted by calling M-x TeX-clean.