Others in evacuation areas have not been so lucky, as large parts of the city remain under water.
The overflowing River Vltava assaulted Prague earlier this week, causing the worst flooding in 200 years, as rising waters brought damage and deaths to places across central Europe.
The head of the European Commission, Romano Prodi, visited Prague to survey the billions of dollars worth of damage, and the EU has already pledged about $50m in aid.
But that is expected to cover just a fraction of the cost of repairing homes and businesses across the Czech Republic, where the rising waters have forced 200,000 to flee their homes.
The surge of water that inundated parts of Prague is now sweeping downstream to the River Elbe and adding to the flooding in the historic German city of Dresden, where about 14 people have been killed.
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Across Europe, more than 100 people have died in two weeks of flooding, including 60 people in Russia.
In Slovakia, floodwaters in the River Danube were almost 10 metres deep in the capital, Bratislava, and the nearby town of Devin was completely cut off by water.
Co-ordinated response
While in Prague, Mr Prodi said representatives of the governments of Germany, the Czech Republic, Austria and Slovakia will hold talks on Sunday with the European Commission "in order to co-ordinate our action".
He added that "member states and non-member states will be treated in the same way."
The Czech Republic hopes to join the EU in 2004.
Mr Prodi surveyed the damage from a helicopter, accompanied by the Czech President, Vaclav Havel.
In Prague's southern Smichov district on Friday, the first people were being allowed back to their homes - only to find their houses and possessions completely covered in thick piles of wet mud.
But many of the 45,000 Prague residents forced to flee were still not allowed to return, even as the floodwaters continued to recede.
Residents of the Holesovice area, for instance, spent hours queuing for permits to visit their homes, but were not allowed to stay because there was still too much water there.
The working-class Karlin area remained completely closed, as emergency workers paddled around on inflatable rafts.
Many areas of the city remain dangerous and several more buildings are expected to be demolished after at least three collapsed, including a four-storey house.
Harder-hit areas
While the historic centre of Prague was largely spared from massive flood damage, other parts of the country were harder hit.
The south Bohemian town of Cesky Krumlov - a Unesco world heritage site - has appealed for help. Around half the buildings in the town's historic centre have been flooded.
In Zalezlice, north of Prague, 90 of the village's 120 buildings are reportedly damaged, and as many as 30 have been demolished.
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