Before the place closes, I might have a couple more opportunities to get down to Guantanamo Bay. Nothing very much has changed. Some of the ­soldiers have become disillusioned, knowing that their orders place them on the wrong side of history. They talk more, they try to make life a little easier on the prisoners. Their commanders have become more dogmatic, if that were possible, like terriers who refuse to give up a bone.

In a way, I am going to miss Guantanamo. It's an odd ­notion, but I've been there more than 20 times, more than six months in all. Sometimes, the true joy of tilting at windmills comes when there is an ogre in the White House. Now they are gone, George W Bush, Dick Cheney and Donald Rumsfeld, the entire Axis of Evil.

Only a few days ago, on 20 January, Americans welcomed in the new year with the inauguration of Barack Obama. The new president immediately demonstrated that he means business, taking a break between dances at his ten inaugural balls to start issuing executive orders. The first 24 hours saw four decrees: the closure of Guantanamo Bay (within a year), a review of US detention policies (including the closure of CIA "black sites"), a review of US "transfer" policies (the euphemism for extraordinary rendition), and an evaluation of what position the administration should take in the case of Ali al-Marri, the only person held in extrajudicial detention on US soil for more than seven years in the "war on terror". Obama did more for the rule of law in one day than George W Bush did in eight years.

However, while this may herald a new dawn, we are very far from the end of the day. If there is one lesson that must be learned from Bush's catalogue of mistakes it is that we should not go hanging up the "Mission Accomplished" banner in too much of a hurry. Bush made his infamous announcement on the USS Abraham Lincoln on 1 May 2003, only 41 days after the invasion of Iraq. Almost six years later, it is sobering to note that more than 96 per cent of the US and coalition casualties came after Bush claimed that it was all over.

The battle for human rights is no more easily won. It is folly to think that Obama can sign four orders and fix an entire era of human rights abuses. A president, no matter how well-intentioned, can only achieve his goals if he has the necessary information and political support. In terms of information, Obama's limited sources have to be a concern. With each policy review that he has ordered, he has named the players who will issue the report: the attorney general, the secretary of defence, the secretary of state, the secretary of homeland security, the director of national intelligence and the chairman of the joint chiefs of staff. For the most part, these are the very institutions that created the problem in the first place. Nowhere does this take into account those who have struggled for change. There are plenty of interest groups opposed to a close analysis of the recent past; others remain convinced that al-Qaeda presents a different paradigm to anything previously encountered, one where the rule of law must give way.

Closing Guantanamo Bay will be a challenge, not least in terms of determining what will be done with the 240 prisoners detained there. The first group is the easiest – the 140 or so prisoners who can just be repatriated. Ninety-seven are from Yemen, and they would be home already if only the Bush administration had talked to President Saleh.

The second group are refugees who need resettlement: there are around 60, most of whom were picked up in Pakistan for bounties. Here, Obama needs help from his allies to offer them sanctuary, and it is sad that the British Foreign Secretary, David Miliband, announced a few days ago that Britain felt it had done enough already. A country that played so integral a part in supporting the mess created by Bush might feel a greater obligation to clean it up.

Last, there is the group of prisoners who will be tried, perhaps 40 of them. President Obama has ordered that the Guantanamo military commissions be suspended. Now looms the struggle over the formulation of a process to replace them. Even liberals in the US are talking about a security court, a ­notion that would sound Orwellian were it not for the fact that Britain already has such a body - SIAC, the Special Immigration Appeals Commission, with all its secrecy and its special advocates, all beyond the public eye.

Obama has also ordered the closure of CIA prisons. This is an interesting comment on his predecessor's candour, since Bush assured us in September 2006 that there were no more prisoners in CIA detention. Indeed, there is no definition of what a CIA prison is: none has ever been designated as such. The overwhelming majority (more than 99 per cent) of the, roughly, 20,000 prisoners still held in US custody, beyond the rule of law, have never been in a "CIA prison". Guantanamo is not a CIA prison. Bagram air base is not a CIA prison, yet the US military continues to hold 680 prisoners without any due process.

What we do know is that, while in US custody, prisoners disappear. Reprieve, together with other human rights organisations, drafted a report called Off the Recordwhich featured 39 people who have vanished in US custody. Only two have surfaced; 37 remain ghosts. The story of Ibn Sheikh al-Libi is an example of how the osmotic pressure of politics can result in prisoners being shuffled quietly off to a terrible fate. Al-Libi was seized in November 2001 and soon rendered by the CIA to Egypt, where torture elicited the "fact" that al-Qaeda and Saddam Hussein were in league over weapons of mass destruction (WMD). Bush cited this as a reason to invade Iraq; the then secretary of state Colin Powell repeated it in the UN. When 14 "high-value detainees" appeared in Guantanamo Bay in September 2006, Ibn al-Libi was not among them; what he might say to a lawyer was just too embarrassing for the administration. So he was rendered to disappear in Libya, where Reprieve has now tracked him down. His story must be told - both to expose the consequences of torture and how Libya is being used to spare Bush's blushes.

Notwithstanding such important individual stories, the directive to close CIA prisons is only of passing relevance. There is also the question of the proxy prisons. The outsourcing of torture and imprisonment was one of the greatest horrors of the Bush years, and there are proxy prisons that have never been part of the public debate, including a particularly unpleasant one in Uzbekistan. Other countries – most notably Jordan and Egypt – continue to serve secret American interests.

It would also be unwise to assume that Obama's policy review is going to eliminate the practice of rendition. This was not a Bush brainchild; as far back as Ronald Reagan, suspects had been "snatched" - the preferred term - from abroad. There was enthusiasm for rendition during the Clinton era. Richard Clarke, counter-terrorism tsar to both Democrats and Republicans, relates an infamous story in his book Against All Enemies:

The first time I had proposed a snatch, in 1993, the White House counsel, Lloyd Cutler, demanded a meeting with the president to explain how it violated international law. Clinton seemed to be siding with Cutler until Al Gore belatedly joined the meeting, having just flown overnight from South Africa. Clinton recapped the argument on both sides for Gore: Lloyd says this. Dick says that. Gore laughed and said, "That's a no-brainer. Of course it's a violation of international law, that's why it's a covert action. The guy is a terrorist. Go grab his ass."

The euphemisms - "rendition to justice" is a favourite one, when someone is "snatched" and brought to face trial in the US - cannot disguise the fact that there is no legal distinction that sets it apart from kidnapping.

President Obama has ordered an end to torture, requiring that all interrogations abide by the Army Field Manual. Yet the ink was barely dry on his directive before talk of adding more coercive techniques to the manual began to surface even from within the Obama administration itself, possibly as a sop to right-wing critics. Obama also said nothing about accountability. With a wink and a nod, before his inauguration, there were signs that he had already come under pressure from both sides of the aisle not to look too carefully at the criminal practices of the Bush administration. Nobody in Congress seems to have the stomach for a bloody inquest, and I believe the Senate leadership have indicated that inquiries are not on their list of priorities. Obama's reticence is understandable enough. He is embarking on a daunting mission, and he must seek allies where he can find them. Digging up the skeletons of the past might have suited the Democrats in the run-up to the election, but if they want Republican co-operation now, the prospect is less appealing.

The setting up of a Truth and Reconciliation Commission, to ensure that the truth comes to light, both for the peace of mind of the victims and so that history can record the mistakes, would be one option open to the new president, and there is no legitimate argument against it. But such a commission will not easily be born. A systematic structure of secrecy - couched in national security terms - may be the most dangerous and long-lasting legacy of Bush and Tony Blair. I have a US security clearance, and while I obviously cannot reveal classified material, I can state without hesitation that the overwhelming majority of it would not remain hidden in a sane world.

Looking to the future, it is enormously exciting to have a US president who is so powerfully in favour of human rights. But it is unclear whether he could sustain his approach in the face of (for example) a further terror attack on US soil. Unfortunately we should not discount the possibility of such an attack. Al- Qaeda must realise that a decent president is a danger to their cause, just as Bush's policies provided the most effective recruiting sergeant to their banner that they could imagine.

Clive Stafford Smith is the director of Reprieve, the UK legal action charity that uses the law to enforce the human rights of prisoners, from death row to Guantanamo Bay. For more information, see www.reprieve.org.uk, or contact Reprieve, PO Box 52742, London EC4P 4WS. Tel: 020 7353 4640