Those who had been accused but not come forward to confess were usually imprisoned, sometimes without even knowing the reason why with their property was confiscated in order to pay for the incarnation and trial.
Eventually, an interrogation would take place. This often involved torture, however, there were some very strict rules that had to be adhered to. Breaking the skin was a big no-no, therefore other methods were used.
The Rack was a favourite, as it would tear joints but crucially the skin did not tear and an early form of waterboarding which involved a rag being stuff in the victim's mouth and water being poured on it which gave the impression of drowning.
Some people after undergoing these treatments would confess and if it happened after the torture had actually stopped it was considered to be "under their own free will" they would then have to make a public declaration of their guilt and accept punishment, this ranged from a fine or 5 years hard labour in a rowing galley (usually meant death).
Those who did not confess or did so during torture faced tougher penalties.
The ultimate punishment was burning at a stake - this is the lasting image of the Inquisition.
The recorded number of people killed have ranged from 30,000 to millions, however, in 2000 the Vatican apologised for the violence and deaths caused but disputed the number of people affected.
It seems that the legend surrounding the Inquisitions had included people executed or tortured by the state Courts as well. The Pope made clear that the rules of torture from the Church clearly said it could only last for 15 minutes and a doctor should be present at all times - it tended to get out of hand when other bodies got involved.
The lower figure is approximately 1% of the 125,000 people interrogated died at the hands of the torturer or executioner - so still significant but nowhere near some of the wild claims (one I read suggested they had executed 3.5 million people, this in a Country which at the time had a population of just 7 million).