A method for regulating execution of an application program includes a process for preparing the application and a process for executing the application. The preparation process divides the application program into related segments and encrypts instructions of at least one segment, positions encrypted instructions in at least two discontiguous regions within an executable file, and associates header information with at least one discontiguous region. The execution process initiates execution of the protected application when at least a portion of the application instructions are available to the computer only in encrypted form. Also provided are systems and methods to allow debugging of code extensions to protected applications without sacrificing protection of the application. A Secure Debugger allows extension developers to examine memory and set breakpoints in their own extensions, without permitting them to view information in the rest of the protected application.