Why Obfuscate?
Most people obfuscate their code for the following reasons:
1) To protect their software from crackers so that they can't see your code.
2) To make your malicious file FUD (obfuscation is a last resort for FUD-ing process)
Obfuscation doesn't affect how your software works, so don't worry.
Step one:
Download {smartassembly} from this thread:
http://sharesend.com/8tp6aStep two:
Install {smartassembly}. I won't go into details here.
Step Three:
Run {smartassembly} and click the "New Project" button. Now click "Browse Assembly". Select your binary/exe. You can set the final build destination if you want by clicking the "Set Destination" button. Here, we will set the destination to Desktop.
Step Four:
Choose the settings in the pictures:
Check Obfuscation:

Scroll down and check "Control Flow Obfuscation":

[OPTIONAL]Scroll down and check "Strings Encoding". Do this if you want to protect personal information such as Emails and Passwords.

Step five:
Now click the build button on the lower right corner of the window.
Wait while it gets built.
Congratulations, you have obfuscated your code.