By the 1950s and 1960s the Soviets had an extensive and decades long reservoir of experience from the NKVD and SMERSH in 'filtering' (interrogating) Soviet citizens accused of Espionage.

Simply put, denying someone sleep for more than 72 hours, keeping them hungry and cold works to break down almost everyone. Added stressors included making them sit on the edge of a chair or on a stool and verbally and physically abusing them if they fail to maintain this uncomfortable position. Things could be done at random times (like feeding a prisoner twice in a couple of hours, then denying food for 36 hours), or locking them into 'coffin' cells (too small to sit down in, ceiling too low to fully stand up) leading to agonising cramps. Simple, but highly effective to break down psychological resistance.

All these facilities were still in place after the fall of Stalin and the reduction in the scale of the labour camps, and most of the personnel were kept in place outside the senior staff. The greatest change from the Stalinist period was that physical violence was comparatively rare as the interrogators had much more time to extract information from each detainee, and most of the genuine sadists had been removed from their positions.

A really good place to start is Anne Applebaum's Gulag, but I could list many further compilations of primary sources if you want a very depressing read. Christopher Andrew's KGB: The inside story is also excellent.