Generating executables programmatically

Question

I am creating a Ebook creator in C# as a project and it needs to create standalone executable ebooks.
The creator app will run on the users system and allow them to choose the contents of the 'ebook' from files on the system. I concieve these being compiled into a executable that acts as a viewer for its content. The same concept is used all over the place but I cannot understand how to code the executable generation part into my existing creator app which itself is compiled by Visual Studio. Is there a namespace providing classes that could help me? So far I havent found anything concrete in my searches on the net. I have looked into the structure of Portable Executables but do not know how to code them. If someone could point me in the right direction I'd be eternally grateful.
Many thanks for any replies

noodleguy