I post this so that I can find this solution later by googling even though this is my own post if by chance I forget how to solve the same problem in the future. Well this is about using custom control within Prism solution. In my PRISM solution, I used WPF Toolkit control in one of my module. I compiled my solution and it was compiled succesfully. But every time I ran it, I always got this exception message:

System.Windows.Markup.XamlParseException occurred
Message=Could not load file or assembly 'WPFToolkit, PublicKeyToken=null' or one of its dependencies. The system cannot find the file specified.

Well, I have added WPFToolkit.dll to my module's reference list, so what's the problem? I couldn't figure it out. I googled and found this post then I realized that I haven't added those dlls to my Shell project (that is project that contains bootstrapper). Of course, it wouldn't be found anywhere since the shell project is the one that load everything else. So, I added the references in my Shell project, and it just worked!