Abstract: A method for permitting software optimization tools, software instrumenting tools and other analysis tools to re-write executables having mixed instructions and data uses a data structure having an entry for each multi-bit word in an executable file. Each entry of the data structure includes a number of flags that are set to identify the type of the multi-bit word in the associated line of the executable file. The types include instruction, data and unclassified. Each entry also includes a flag that indicates that the multi-bit word should not be optimized and a flag indicating that the multi-bit word is a problem branch. The no-optimize and problem branch flags may be used to identify multi-bit words that may be either branch instructions or data, and to ensure that such multi-bit words are not affected by optimization or other rewriting of the executable. In addition, a problem fall through flag is provided to maintain program flow for possible fall through code segments.