SmartAssembly creates one assembly at a time.

If you want to obfuscate several assemblies without merging them, you need to create several projects.

If you have a web application with several small DLLs (App_web_*.dll), consider merging them in a single assembly using aspnet_merge.exe, and then protect the resulting assembly with SmartAssembly.

See http://msdn2.microsoft.com/en-us/library/aa479044.aspx for information on how to use aspnet_merge.exe