I understand that you want to encrypt the .mlapp file and package
The following 3 ways will help you to achieve this:-
1) Use MATLAB Compiler to compile everything. MATLAB Compiler encrypts using AES. You can refer to below two links for more understanding on how to use MATLAB Compiler to encrypt.
2) Use your own encryption scheme. It will be necessary to decrypt the code before it can be executed. You can refer to below link.
3)Use pcode which obfuscates code (makes it more difficult to access and understand) but does not actually encrypt it. You can refer to documentation of pcode.
