Colonel Kurtz was modeled after real-life CIA operative Anthony Poshepny

Yes, the movie was loosely based on Joseph Conrad's "Heart of Darkness" switched to the Vietnam setting of the late 60s and Colonel Kurtz (Marlon Brando) was based on the successful ivory trader Mr. Kurtz from that book.

However, the CIA Paramilitary Operations Officer Anthony Poshepny was also used as a real-life blueprint for the character and was more relevant to the setting of the film since he functioned in remote areas of Southeast Asia wherein he worked with tribes.

More specifically, Poshepny was dispatched to train a secret CIA-funded paramilitary force of Hmong hill tribes in Laos during the Vietnam conflict to fight the North Vietnamese and Pathet Lao forces. He paid Hmong combatants to bring him the ears of slain enemy soldiers. Similar to Kurtz in the movie, he dropped severed heads in enemy locations as a grisly form of psychological warfare.

https://en.wikipedia.org/wiki/Anthony_Poshepny
https://www.businessinsider.com/10-things-you-probably-never-knew-about-apocalypse-now-2015-10