Building App file from obfuscated exe

Dear all,
I would like to build a program in 3 steps,
1. create the .exe file,
2. obfuscate and secure the .exe file. This I would take from the bin-folder.
3. create a .app file from the obfuscated .exe file.
I don't know how to execute the 3rd point. Is it maybe possible to do this from the shell with a mono command?
Thanks in advance
robin