A system and method for providing exceptional flow control in protected code through memory layers. Code is generated. The generated code includes a sequence of normal operations and is subject to protection against copying during execution of the generated code. The generated code is instantiated as a master process into a master layer in a memory space. The master process is cloned by instantiating a copy of the master process as a child layer in the memory space. Execution points within the generated code are identified. A copy of at least a portion of the generated code containing each execution point as an exception layer is instantiated in the memory space. The generated code in the exception layer is patched at each identified execution point with operations exceptional to the normal operations sequence and which are performed upon a triggering of each execution point during execution of the generated code.