For innocent victims of miscarriages of justice languishing in prison, it must be hard to maintain faith in the criminal justice system. What hurdles do wrongly convicted people face, in trying to clear their name and after securing their release? Forty years after his murder conviction, James Hanratty's supporters are engaged in a quest to clear his name. The Court of Appeal reaffirmed guilt on the basis of DNA evidence last month, and the case is now heading to the House of Lords.

Hanratty was sent to the gallows in 1962, for the murder of Michael Gregsten and the attempted murder of his lady companion, Valerie Storie. Public outcry after his hanging marked the death knell for capital punishment here. For his supporters, a posthumous pardon and vindication of their struggle is the most they can expect.

The wheels of justice are not infallible, and causes célèbres demonstrate the failings. As at 31 March 2002, the Criminal Cases Review Commission, established in 1997, had handled some 4,830 applications from people claiming to have suffered rough justice in criminal courts. Of these, 161 resulted in referrals to the Court of Appeal and 64 convictions were quashed.

The commission was set up to investigate suspected miscarriages of justice, replacing the ad-hoc discretion of the Secretary of State. David Sonn, partner at specialist criminal practice Sonn MacMillan, explains that it "investigates a case if new evidence comes to light or there has been a defect in the trial process. It has significant powers of investigation and referral back to the Court of Appeal." The caveat is that it is a last resort: "An application can only be made when all other appeals have been exhausted." If you have had your case referred back, their endorsement, Sonn believes, "should stand you in good stead".

Sonn has first-hand experience of the tribulations endured by wrongly convicted clients. In 1999, he represented Chetan Popat in an application to the Commission in relation to his convictions for attempted rape and indecent assault. This meant lengthy preparation at ungenerous rates. Fortunately, the Commission referred Popat's case back to the Court of Appeal, which quashed the conviction. At retrial, the jury found in his favour.

Michael Mansfield QC, now representing victims' families at the Bloody Sunday Inquiry, has appeared in some high-profile miscarriage cases. He recommends that "in order to get a successful application it is advisable to have a solicitor on board to put in a petition". Mansfield's portfolio includes Hanratty, the Guildford Four, the Birmingham Six and the Hyde Park bombing case. In the latter, Danny McNamee's conviction of conspiracy to cause the explosion in July 1982 was quashed on appeal.

He cites with authority circumstances that can lead to review: "The major factor is substantial non-disclosure." Also relevant are "improperly obtained confessions, flawed identification or scientific evidence". In McNamee's case, "the Court of Appeal, found the conviction unsafe because of questionable fingerprint evidence". Although the appeal process may lead to freedom, psychological pressures can be overwhelming. Mansfield says the greatest "iniquity is if you protest your innocence then you forfeit parole. This often means that you end up serving more time than the person who did commit the crime."

Similarly, Elkan Abrahamson, a solicitor specialising in miscarriage cases, points out that prison conditions for those who protest innocence could be worse than those of fellow inmates. Because they do not accept guilt, "deniers" do not progress through a prison system that expects offenders to show remorse. He observes, too, that some victims of miscarriage "are inadequate in some way, such as having learning difficulties". This could make them susceptible to wrongful conviction. Money is another issue. Ungenerous legal aid rates probably deter firms from handling this work. Mansfield says that appellants need to "have a very committed solicitor", and the government-financed Commission is "seriously underfunded and there are not enough case officers".

If freedom is secured, the nightmare is not necessarily over. Abrahamson describes two obstacles for vindicated appellants. First, "there is no superstructure as such". Rehabilitation is a concern. He would like to see those exonerated offered "therapy or counselling to come to terms with spending a lot of time in custody".

The National Association for the Rehabilitation of Offenders confirms that while they help all former prisoners, there is no special scheme for victims of miscarriage. NACRO report a re-offending rate for convicted criminals of 50 per cent, highlighting the need for support mechanisms.

Abrahamson states that "the other problem is if someone is in prison and is expecting to get out because of miscarriage, the prison cannot prepare a release package". Normally, probation services know the release dates of prisoners. With "deniers", this is unknown. Where financial compensation is offered by the Home Office, this is "on an ex gratia basis" and "it takes a long time to get the money".

Shortly after I spoke to Abrahamson, the Home Office announced a 12-month pilot scheme to redress the hardship of prisoners who have successfully appealed against conviction. Administered by the Citizens Advice Bureau, their representatives will make prison visits before appeals and provide "immediate practical advice and support following release to help them access services and reintegrate into society". The jury is out on this initiative.

The national charity Unlocked works alongside the Home Office and prison services, helping ex-offenders and victims of miscarriage rebuild their lives. Bobby Cummines, Unlocked's deputy chief executive, says it is "run by ex-offenders for ex-offenders". He is sanguine about attitudes towards former criminals and sees a change in society's perception as vital. Special understanding is needed for people who have "experienced a brutal, and barbaric system, knowing they are innocent".

Even temporary incarceration causes disruption. "If someone is on remand, the council can say that while you are in prison you must sign away your home and be relocated when you come out." Ex-offenders can find themselves "at the bottom of the list with a destroyed job and their marriages or relationships broken down".

Mansfield makes the point that there are a plethora of groups, such as Gloucester against Injustice and Innocent, offering support. While acknowledging their contribution, his view is that "to provide a powerful force it is important to act with one voice". He advocates one umbrella organisation.

In the Guinness case – ongoing after 12 years – the defendants sought redress from the European Court of Human Rights, having exhausted local remedies. Some cases are still taken to Europe, but this route has been less necessary since the incorporation of the Human Rights Convention into domestic law by the Human Rights Act 1998. Besides, few convicted individuals are likely to have their means of funding.

The convictions in 1990 of Saunders, Ronson and Parnes were referred back to the Court of Appeal by the Commission, but with less success. Their review applications were made some 10 years after sentencing. Keith Oliver, the solicitor who represented Saunders says: "These cases do take a long time to prepare, visiting events which don't replay in short-hand."

Talking about high-profile trials, he adds: "The events under enquiry may last several years. It is unfair to expect the prosecution to encapsulate them. If you are dealing with people's liberty, you need to look at things microscopically."