I'm creating a program in python (2.7) and I want to protect it from reverse engineering.
I compiled it using cx_freeze (supplies basic security-  obfuscation and anti-debugging)
How can I add more protections such as obfuscation, packing, anti-debugging, encrypt the code recognize VM.
I thought maybe to encrypt to payload and decrypt it on run time, but I have no clue how to do it.
There's no way to make anything digital safe nowadays.
What you CAN do is making it hard to a point where it's frustrating to do it, but I admit I don't know python specific ways to achieve that. The amount of security of your program is not actually a function of programsecurity, but of psychology.
Yes, psychology.
Given the fact that it's an arms race between crackers and anti-crackers, where both continuously attempt to top each other, the only thing one can do is trying to make it as frustrating as possible. How do we achieve that?
By being a pain in the rear!
Every additional step you take to make sure your code is hard to decipher is a good one.
For example could you turn your program into a single compiled block of bytecode, which you call from inside your program. Use an external library to encrypt it beforehand and decrypt it afterwards. Do the same with extra steps for codeblocks of functions. Or, have functions in precompiled blocks ready, but broken. At runtime, utilizing byteplay, repair the bytecode with bytes depending on other bytes of different functions, which would then stop your program from working when modified.
There are lots of ways of messing with people's heads and while I can't tell you any python specific ways, if you think in context of "How to be difficult", you'll find the weirdest ways of making it a mess to deal with your code.
Funnily enough this is much easier in assembly, than python, so maybe you should look into executing foreign code via ctypes or whatever.
Summon your inner Troll!
protect python code from reverse engineering