Is it a good design to have multiple masterpages in an application. I am building a website using Asp.net MVC with different type of users like, admin, employee, general user, etc
And every user once logged in have different type of controls on the website, so I was planning to use different master page for each user.
Yes it is a good design, and make sure to layer them appropriately. Master pages specific to controllers should be placed them in the appropriate view folder.