Munoz took office in January 2014, investigating judges have sent some 400 cases to prosecutors, according to the Interior Ministry.
For Munoz, a silver-bearded, stone-eyed judge who gained a reputation for maverick decisions during his 31 years on the bench, this push is needed to close one of Chile’s darkest chapters.
"For the victimisers, this means the state has not forgotten what you’ve done, and you will be punished," said Munoz, a law student early in the dictatorship who went on to investigate human rights cases as a judge.
"There will be no closed doors behind which you can hide."
Munoz regularly meets with Chile’s investigating judges, prodding them to get data, dispensing firm feedback, and setting deadlines.
He has also appointed a liaison to the military, who is tasked with extracting information from officers who lawyers and rights activists say have a habit of protecting their own.
"In the past, investigators would ask the military for information, and it would come back nine months later saying ‘that document has been incinerated or destroyed’," said Alejandro Solis, the current liaison and a former human rights judge.
"But during that time, nobody would actually ask, ‘Well, who destroyed it?’"Investigators have also been aided by modern forensics that can now identify remains and determine foul play with smaller body fragments and less genetic material than before.
"Now, if we find remains dated from the seventies or eighties, we deploy anthropologists, archaeologists, geneticists, forensic photographers - a multidisciplinary team," said Patricio Bustos, the head of Chile’s forensic service who himself was tortured under the dictatorship.
Some politicians on the right still defend Pinochet’s legacy, saying the 1973 coup saved Chile from President Salvador Allende’s Marxist agenda.
However, polls show support for Pinochet has declined in recent years and there is little vocal opposition to the pursuit of ex-military personnel accused of human rights violations.
Defence Minister Jose Antonio Gomez has voiced support for the prosecutions, saying the military must make itself "an institution for the future."
Even so, many Chileans believe the courts are still far from guarantors of justice.
Though there is no statute of limitations for human rights violations in Chile, there are signs the passage of time between a crime and its prosecution is leading to softer sentences.
"On the one hand, we’re putting through cases faster and they’re being resolved," said Solis. "But some families say, ‘Right, but what justice is this?’ This man killed my husband and son and he’s condemned to spend three years in his own home’.
"Rights activists and victim groups also worry that the drive may slow, or even grind to a halt when Munoz’s term ends in January 2016."
Under the current court things are better," said de Negri. "But that doesn’t mean the whole government has a clear commitment to human rights."