They were referred to by their first name, their last name or a nickname.

Charlie, the common nickname for the Viet Cong (which in turn was a nickname in itself. The proper name would be the People's Liberation Armed Forces of South Vietnam or the Armed Wing of the FNL) guerrillas, derived from the letter C (meaning Cong, from VC - Victor Charlie) of the NATO phonetic alphabet. The use of Charlie as a nickname for the Viet Cong guerrillas was actually short for Charlie Cong and Victor Charlie which was also used by men in the field to refer to their enemies.

Despite it being a common nickname for the Viet Cong, Charlie was in widespread use since Charlie could in many instances stand for the name of a company (Charlie Company, etc.) or command for example. One such instance would be the nickname Charlie Bird for a command helicopter.

It's also interesting to note that there were many different nicknames for the Viet Cong used by US troops. The book Vietnam War Slang: A Dictionary on Historical Principles by Tom Dalzell (Routledge, 2014) identifies nicknames such as Black Hat, Clyde, and variations of Charlie such as Uncle Charlie and obviously, Charles. This is of course excluding the downright racist nicknames given to enemy combatants by American troops.