Thousands took to the streets Friday in protests calling for compensation and the release of revolutionaries imprisoned through military or civilian courts since last year's popular uprising.
The demonstrations, set to take place in Cairo, Suez and Alexandria, were initially called for by Efrag ('Release') Movement, an umbrella group working to free prisoners of conscience, together with the No Military Trials for Civilians campaign, Popular Socialist Alliance Party, the Revolutionary Socialists, the Social Democratic Party's youth wing and the Egyptian Wave Party (a party established by the Muslim Brotherhood's young cadres).
"The Friday marches are also putting pressure on the authorities to grant moral and financial compensation for the long-term effects on the political prisoners," explains lawyer and activist Ragia Omran, who has represented many of the detainees.
Over 12,000 civilians have faced military trials since Mubarak's resignation, a practice which is illegal under international human rights law and sees defendants summarily tried by military judges with little to no legal representation.
Military sentences are administered quickly, often on trumped-up charges. Nadia Hassan from No Military Trials for Civilians described one case where a trial took place in a kitchen, due the lack of court space.
Until May 2012, Egypt was under Emergency Law, which criminalised political protests, consequently hundreds of demonstrators have also been tried in civilian exceptional courts.
Although no new cases are being referred to these tribunals, Ahmed Seif El-Islam, founder of NGO Hisham Mubarak Law Centre explains, anyone who was tried before emergency law expired, continues to face trial in front of these courts.
The lack of transparency within Egypt's different courts, prisons and police stations makes it hard for rights organisations to locate and track political prisoners.
Over a thousand people are still missing since the 18-day uprising. "The numbers that we have found is comparatively very small to the number of people unaccounted for," says Amr Iman, a lawyer working with No Military Trials for Civilians to secure the release of detained activists, "Some we have found in the morgue, some in the prison but we still don't know where the rest are."
Hanlayhom ("We will find them") initiative was launched earlier this month to find those who have disappeared at protests and at the hands of the security forces.
Revolutionary and human rights groups hoped for greater judicial transparency and the release of political prisoners following the appointment of a civilian president, particularly as Mohamed Morsi himself was imprisoned by the Mubarak regime in 2006 for his political activity.
Since assuming office, Morsi has set up a presidential "Civil Rights Protection" committee, to look into all cases of civilians detained by military authorities.
Members of the group include key revolutionary figure Seif El-Islam.
The committee's reports led to Morsi's recent wave of presidential pardons. Early in August, the president ordered the release of 572 citizens detained by military authorities since February last year.
"Morsi also released around 25 political prisoners imprisoned during Mubarak's era," explains Maha Maamoun from the Hisham Mubarak Law Centre, "but these were largely considered to be Islamist jihadists, which has sparked some concerns about their release."
After Ramadan, another 58 were released, including six from February protests against the state handling of the Port Said football disaster and well-known activist "Sambo" Mohamed Gad Al-Rab, who was arrested during the 28 June 2011 clashes with police on Cairo's Tahrir Square.
Although civil society groups welcomed the move, many criticised Morsi for not granting amnesty to those released.
"Their verdicts were suspended so they still have criminal charges against them," explains Maamoun, "This means if they commit another 'crime' they will be back in jail, facing the combined punishments of the two verdicts."
There is no distinction made between those prosecuted for criminal behaviour and those arrested for their political beliefs or activities.
The issue is further muddied by the fact that many political prisoners are facing non-political charges, which are sometimes false, such as possessing weapons or drugs, making it harder to identify them as prisoners of conscience.
"The presidential pardon simply decreased Sambo's sentenced from five years to one year," explains Iman, who is representing Al-Rab.
This, however, means Sambo retains his criminal record for life.
Ongoing financial worries is a problem political prisoners face as many not only lose their job whilst serving time in prison but also cannot find work following their release due to their criminal record.
This is one reason why activist groups are pressuring Morsi to grant reimbursement and amnesty.
Compensation for the emotional trauma suffered is also top of the list.
"The treatment of detainees is bad and political prisoners are often treated worse," explains Iman.
Adel Ramandan, a legal officer at the Egyptian Initiative for Personal Rights (EIPR) working with military trials victims, described what happened to his cousin Muaty Abu-Arab, one of the first protesters to be arrested during the revolution on 3 February, 2011.
Aside from the "usual torture package" of beatings, verbal humiliation and sporadic starvation, Ramadan explained, Abu-Arab witnessed some really extreme cases that “went beyond our ideas of torture.”
“People were covered in water and electrocuted, sometimes to death and thrown in the desert,” Ramadan said, relating his cousin’s experiences.
For Sambo, the "special" treatment of political prisoners came in the form of emotional abuse, in addition to the physical beatings.
"If someone sent him a letter the officers would destroy it in front of him," Iman explains, "They'd taunt him by asking him if he thinks he's a hero."
Children are among the political detainees. "We know at least three minors who are currently in prison after facing military trial but we cannot find all of them," explains Omran.
One such prisoner, Islam Harby, who was 15 years old when arrested last March by military police in the Moqattam district of Cairo, is still being held with adults 18 months later at Tora prison.
As it stands after the latest pardons, there are around 50 known political prisoners still in jail, Seif El-Islam explains, in addition most of those now facing trial for their political activity are in ordinary civilian criminal courts.
As far as the human rights groups can confirm, the majority of protesters detained during the 18 days and in the subsequent sit-ins on Tahrir Square early last year have been released.
In the last two days, the courts gave a verdict on protesters arrested on 9 September outside of the Israeli Embassy in Cairo during demonstrations against the murder of an Egyptian soldier. "There were 76 individuals in total, 74 got a year suspended prison sentence, so still live under threat of being jailed in the future," Iman explains.
The majority detained following the Maspero clashes with the military on 9 October, which saw 27 protesters killed, have been released. "Only two from Maspero, who admitted to holding weapons when they were arrested, are still in prison," says Omran.
The lawyers confirm that most of those arrested during this May's military attack on a protest at the Ministry of Defence building in Cairo have also been released. On 4 May, the single largest wave of detentions in a post-revolution demonstration saw around 300 civilians hauled in front of military courts.
Iman, who represented the 16 women incarcerated, confirmed that all of them, bar one currently in jail, were given suspended sentences. Ragia Omran added that the majority of the others either received suspended or decreased sentences of between three to six months.
The biggest battle human rights advocates currently face is defending around 600 individuals still facing trial for their involvement in Mohamed Mahmoud Street and Cabinet clashes with security forces in November and December last year, explains Seif El-Islam.
The five-day clashes between protesters, military police and the central security forces were some of the bloodiest battles seen post-Mubarak's ouster and resulted in the deaths of over 60 civilians.
The hearings, which are taking place in civilian criminal courts, have been postponed until 19 and 26 October. A decision is not expected any time soon.
The corruption of the Egyptian judiciary remains a problem often contributing to the incarceration of political prisoners.
"There were a number of high profile activists dragged in front of military courts last year like [blogger] Alaa Abdel-Fattah. The judicial system with all of its faces: military, civilian and administrative, needs to undergo a cleansing revolution," Iman says.
Seif El-Islam agrees, "It has been a systematic policy for the state to use the judicial system for its own means, often by promoting pro-regime judges. Consequently majority of the state is still from the old regime."
New legislation is needed to re-organise the court system, Seif El-Islam explains, and the most advisable way to do this is to wait for the newly elected parliament not to use the legislative authority of the president. Morsi's recent assumption of this parliamentary power was denounced by many, who were uncomfortable with the executive authority holding such sweeping legislative powers.
"We need to re-establish our parliament, re-draft our constitution and put society on a democratic track in order to purge the judicial system, which will take at least five years," Seif El-Islam concludes.
Nevertheless, the recent pardons of political prisoners indicate that Morsi is responding to the presidential committee reports. The fact that military court cases are being referred to civilian courts is also a constructive development, Seif El-Islam adds.
The appointment of celebrated reformed judge Mahmoud Mekki as Morsi's vice-president was seen as an unexpected but positive step.
Ahmed Mekki, Morsi's choice of justice minister, who has also been pushing for judicial reform was largely praised. Although he blotted his copybook on Tuesday when he announced that Morsi was considering controversial new emergency laws to combat "thuggery," historically a charge laid against political activists to quell dissent.
Recent court cases against members of the media for "insulting the president" and the Brotherhood have further stepped up fears of crackdowns on political expression.
"We hope Morsi will give dignity to Egyptians both in Egypt and abroad," Omran concludes."In the meantime, we will keep the pressure up until justice is served."