You only get projects and project collections that you have connected to. If you remove them from appearing in Team Explorer, just click on "Configure Team Projects" link and select only the project that you want to appear. Only that project will appear in Team Explorer.
EDIT If you are looking to filter within Source Control Explorer, get the TFS Source Control Explorer Extension. It adds a toggle button "Filter folders by folder mapping". When turned on, it will only display folders in Source Control Explorer, which are mapped to your machine. See below