Methods and a tool or instrument for performing the methods of protecting a computer program with a parameter cloud are disclosed. A parameter cloud comprising a plurality of elements may be created. Called functions of a computer program may have defined expected parameter cloud states so that proper behavior of the called function is achieved when the parameter cloud state is the expected parameter cloud state. An expected parameter cloud state may include a selected set of elements of the parameter cloud having assigned values. Static portions of the called functions may depend on a current parameter cloud state, and calling functions may transform the parameter cloud state prior to calling their respective called functions. The methods and instrument may operate on original source code or post-binary targets of the computer program. A fingerprint may be used to identify a specific computer program from a sequence of state transitions.