Though all these terms are related to the search engine and the optimization of websites and other accounts, there is slight difference which makes them totally different from each other.
Search engine marketing (SEM) is the process of gaining incoming traffic and visitors to the website by purchasing the advertisements on the search engines. SEM can be taken as the paid search to refer to all the paid listings and can be used as the search marketing as well.
Google Webmaster Tools are the prime service of Google to help and track the performance of your site. This free tool is available for the search engine optimizers, content writers and other web professionals to improve their working upon the website.