How do you specify a master page in a web page with code separation?

I have no problem specifying a master file in certain pages of a website when there is no code separation by having the top line state: <%@ Page Language="C#" MasterPageFile="~/MasterPage.master" Title="Welcome" %>. However, when I add MasterPageFile="~/MasterPage.master" to the top line of a web page that has code separation, I get a Server error that says, “Content controls have to be top-level controls in a content page or a nested master page that references a master page.”  So, how can I specify a master page in web pages with code separation?
 Maurice
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