I think I saw this in a TV program a few years back that the Pope of the time confined himself in a semi-sealed room under the Vatican for a long period of time, and surrounded himself with torches and braziers that burnt aromatic substances. Is this true?
Not quite.
When the Black Death struck in 1348, Pope Clement VI was in Avignon, in southern France, where the papacy was based, for various political reasons, from 1309-1378. Initially, he reacted in the way you'd expect a medieval cleric to react, by calling for prayers, penance and big religious processions, in which he himself took part. These public processions seem to have gotten out of hand very quickly though, with thousands of people including flagellants flocking to the streets of Avignon, and seem to have stopped by the summer of 1348.
After this, Clement took the advice of his doctor, Gui de Chauliac, and isolated himself in his chambers, lighting giant fires and torches in an effort to purify the air. He split his time between the papal palace at Avignon and his castle at Valence on the Rhone, but kept the same routine either way. In the end, it worked, and Clement lived for another 4 years.
I'm basing this off Philip Ziegler's 'The Black Death', which I'll add is a fine source for the basic chronology of the plague but is very out of date on the interpretive side. It's the only book on the plague I have to hand at the moment though, but if there's any follow up I can chase things up in the more recent secondary literature.