You could use CodeDOM or Reflection.Emit, also if you are doing this at
compile time, you may want to look at assembly linker (al.exe), when you
are using VS.Net this tool rarely gets used, but you can use it to
create multi-module assemblies, i.e. assemblies that consist of more
than one physical file. Let me know if you are doing this at runtime or
compile time, we'll try and work something out.

http://msdn.microsoft.com/library/default.asp?url=/library/en-us/cptools/html/cp
grfAssemblyGenerationUtilityAlexe.asp

Sijin Joseph
http://www.indiangeek.net
http://weblogs.asp.net/sjoseph