A method and system are provided for deriving a resultant software program from an originating software program having overlapping branches, wherein the resultant software project has either no overlapping branches or fewer overlapping branches than the originating software program. A preferred embodiment of the invented method generates a resultant software program that has no overlapping branches. The resultant software is more easily converted into programming reconfigurable logic than the originating software program. Separate and individually applicable aspects of the invented method are used to eliminate all four possible states of two overlapping branches, i.e., forward branch overlapping forward branch, back branch overlapping back branch, and each of the two possible and distinguishable states of forward branch and back branch overlap. One or more elements of each aspect of the invention may be performed by one or more computers or processors, or by means of a computer or a communications network.