The Tower of London was used as a prison for noble or important people such as political prisoners. Imprisonment was not necessarily uncomfortable, as prisoners could purchase luxuries and fine food from the Lieutenant of the Tower. Torture did take place in the Tower, but had to be sanctioned by the Privy Council, so was not commonly used.
The most common form of torture was the rack: a prisoner would be stretched, causing terrible pain until his joints dislocated and his bones and ligaments snapped. Another was the Scavenger’s daughter, which worked by compressing the body, expelling blood from the nose and ears. Nevertheless, some prisoners held in the Tower for long periods found it as comfortable as their own home. While Walter Raleigh was held there, he had his rooms altered to accommodate his family, and his son was even born there!