Most military aircraft have Mode 1,2,3,4, and now 5, all of various capabilities, of which Mode 3/A (with altitude reporting) is also in common use by non-milit

Most military aircraft have Mode 1,2,3,4, and now 5, all of various capabilities, of which Mode 3/A (with altitude reporting) is also in common use by non-military aircraft. "Squawking" a particular mode, and code in the mode, only means it has been set in the cockpit. An Iranian F-14 would most certainly had both a Mode 2 and Mode 3 capability, so no, an Mode 3 code does not identify it as civilian.