Using SharePoint Designer 2007, you can easily customize your SharePoint Master pages. If you want to create a new master page you can easily do it. To do that first copy the default.master page and rename it to whatever name you want (Master page can be found at "C:\Program Files\Common Files\microsoft shared\Web Server Extensions\12\TEMPLATE\GLOBAL").
Then go to the your SharePoint site and go to Site Settings. Click Master Pages under Galleries category and upload the renamed master page to the Master pages.
Then open the SharePoint Designer 2007 and click on the Open Site in the File menu.
Then copy the url of the your SharePoint site and open it in SharePoint Designer 2007. You can see the master pages of the site in the catalogs folder. Double click on the renamed master page to edit in SharePoint Designer.
Then you can customize that page according to your requirments. If you want to remove some parts in the master page, the best thing is comment those code instead of deleting those in the design mode. The reason is if we delete those in design mode it gives errors in the design mode or when we publish them.
After customizing the page click on Save. If you want to set the customized Master Page as the default master page, righ click on it and select "Set as Default Master Page".
That's all. After that you can use the customized master page for other SharePoint Web Applications too.