To remove a component right-click the project version and select 'Administration | Manage Components'.
Select the component you want to remove and press the 'Remove' button. You will then be given the option to delete the folder in the project version.
If you choose to delete the folder then a changeset will be created deleting the folder containing the component with all its files and folders. If you choose not to delete the folder then the folders and files in the project version will not change, but the link to the component will be removed. So updating these files and folders will no longer update the component version.