I've used sharepoint designer in the past to create my custom master pages. I personally do not like sharepoint designer because it's so buggy (slow, shuts down unexpected, ect). With all the new stuff in VS 2010 for sharepoint is it possible to create a master page from scratch?
I would highly recommend you to start with the Starter Master Pages project by Randy Drisgill over at codeplex - http://startermasterpages.codeplex.com/.
In my openion its the best starting point to create a custom master page in SharePoint 2010...
Visual Studio 2010 does not actually allow you to visually see what is going on with your master page, so it would better to keep SharePoint Designer 2010 as being the best and only tool doing it. It has greatly improved from SharePoint 2007, really had excellent experiences.
You could then use VS2010 to help you build the solution package to properly deploy all artifacts related to your branding solution. See here for a ready solution http://msdn.microsoft.com/en-us/library/gg447066.aspx
Heather Solomon and Randy Drisgill are the references in branding SharePoint, search for their names on the web.
I was able to implement a custom master page using visual studio only. This site helped out a lot. Hope someone else can get use of it as well.