A system and method for transforming a software application comprising binary code and optionally associated data, from an original form to a more secure form. The method includes performing a combination of binary transmutations to the application, and interlocking the transmutations by generating and placing interdependencies between the transmutations, wherein a transmutation is an irreversible change to the application. Different types of the transmutations are applied at varied granularities of the application. The transmutations are applied to the application code and the implanted code as well. The result is a transformed software application which is semantically equivalent to the original software application but is resistant to static and/or dynamic attacks.