Other people have suggested using in.nextLine() to clear the buffer, which works for single-line input. As comments point out, however, sometimes System.in input can be multi-line.
You can instead create a new Scanner object where you want to clear the buffer if you are using System.in and not some other InputStream.
in = new Scanner(System.in);
If you do this, don't call in.close() first. Doing so will close System.in, and so you will get NoSuchElementExceptions on subsequent calls to in.nextInt(); System.in probably shouldn't be closed during your program.
(The above approach is specific to System.in. It might not be appropriate for other input streams.)
If you really need to close your Scanner object before creating a new one, this StackOverflow answer suggests creating an InputStream wrapper for System.in that has its own close() method that doesn't close the wrapped System.in stream. This is overkill for simple programs, though.