applying theme to master page?

[bramemurl]

I know in general themes cannot be applied to Master pages. But I was wondering there can be some trick or way to do so. In my situation I dont want to apply these to the whole site but only on an application. Because in application there are many pages I cant do it manually. In my situation I am also not able to inherit page class. Any suggestion please. This project is in Asp.net 3.5Thanks