Fortunately 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.
So, what intermediate files are deleted? Depending on the type of file being edited, it varies. For example, for LaTeX files, it's
LaTeX-clean-intermediate-suffixes is a variable defined in `latex.el'.
Its value is ("\\.aux" "\\.bbl" "\\.blg" "\\.brf" "\\.fot" "\\.glo"
"\\.gls" "\\.idx" "\\.ilg" "\\.ind" "\\.lof" "\\.log" "\\.lot"
"\\.nav" "\\.out" "\\.snm" "\\.toc" "\\.url")
To know the exact way things can be customised, see the AucTeX manual, especially Cleaning.