Nizar Sassi and Mourad Benchellali, both French citizens, were arrested by US forces in Afghanistan before being transferred to the notorious prison set up in Guantanamo Bay to hold terror suspects after the 9/11 attacks.
They were held there from the end of 2001 until 2004 and 2005 respectively, before being sent home.
A French probe into their case began after they filed a complaint in court.
"The door has opened for civilian and military officials to be prosecuted over international crimes committed in Guantanamo," their lawyer William Bourdon said.
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Despite promises by US President Barack Obama to close the prison, which is located in Cuba's Guantanamo Bay -- an area on the east of the island under US control since a treaty signed in 1903 -- it remains open and still houses detainees without charge.
The US presence at Guantanamo Bay, where it also has a naval base, is one of the major stumbling blocks in Washington and Havana's historic move towards normalising ties.
In an expert report submitted to a French judge last year, lawyers for Sassi and Benchellali accused Miller of "an authorised and systematic plan of torture and ill-treatment on persons deprived of their freedom without any charge and without the basic rights of any detainee."
Just before Miller became commander of Guantanamo in late 2002, president George W Bush's administration approved so-called enhanced interrogation techniques, including placing detainees in stress positions, stripping them, isolating them for extended periods of time and exposing them to extreme heat and cold.
Miller then implemented these methods.
And even though then-secretary of defence Donald Rumsfeld withdrew permission for the most controversial of these interrogation techniques shortly thereafter in January 2003, "under ... Miller's command at Guantanamo, these techniques continued to be used in certain cases," the detainees' lawyers said last year.