The troops were instructed to "traumatise and terrorise" the population to prevent them from supporting any resistance to Ange-Felix Patasse, the Central African Republic president, the prosecution said.
"To do this, he [Bemba] chose rape as his main method," Kneuer said.
A representative of victims told the hearing that a district chief in the capital of Bangui was raped for four hours in front of his wife and children before troops turned to them.
Bemba's defence lawyers argued that he was not responsible for the campaign of torture, rape and murder between 2002 and 2003 as his Congolese Liberation Movement (MLC) forces were operating under the command of Patasse.
"Uniforms, food and money were all provided to MLC troops, not by authorities in the Democratic Republic of Congo, not by Mr Bemba, ... but by the head of state of the Central African Republic," Asad Ahmad Khan, one of the defence lawyers, said.
After the four-day pretrial confirmation of charges hearing, the three-judge panel led by Ekaterina Trendafilova has 60 days to decide whether to go forward with the trial.
Bemba was arrested in Belgium last May.
He fled DR Congo for Portugal in 2007 saying he feared for his life after his fighters had battled the presidential guards of Joseph Kabila on the streets of Kinshasa, the capital, following his defeat in presidential elections.
The MLC was formed to overthrow Laurent Desire Kabila, Joseph's father and DR Congo's former president, during the 1998-2006 war in DR Congo.