When you signup for webmaster tools the google will give you a file name, i.e:
abcd12345ksjsjs.htm
You need to create an empty file (use notepad) and give it that name. Once done, upload the file to you server root so that it can be accessed via the following URL
http://www.yoursite.com/abcd12345ksjsjs.htm
Then verify the site
Remember the file name given here is just an example