Thai authorities have issued arrest warrants for 13 protest leaders and the man the protesters support, former Prime Minister Thaksin Shinawatra.
The group had been charged with inciting a public disturbance and illegal assembly, the warrant said.
The protests have shut down large parts of the capital, Bangkok, for the last three weeks. Clashes on Monday left two people dead and dozens of others hurt.
But on Tuesday, as troops massed, the protesters called off their action.
Overnight the army hemmed in several thousand activists around Government House.
More soldiers then moved in, prompting the protest leaders to call on their remaining followers to go home to avoid further bloodshed.
The protesters support former leader Thaksin Shinawatra, who was ousted by the military in a 2006 coup.
They want the current government, under Prime Minster Abhisit Vejjajiva, to step down and fresh elections to be called.
Mr Thaksin has been living in overseas exile for much of the last three years. Last year a Thai court convicted him in absentia of corruption.
On Sunday he called for a "revolution"; on Monday he told the BBC he meant a "peaceful revolution".
'To save lives'
The Thai court named the ousted prime minister in its warrant.
"Thaksin and his allies were charged by the court for illegal assembly of more than 10 people, threatening acts of violence and breach of the peace," the warrant said.
The charges were punishable by five years in jail, it added. Four of those named have already turned themselves into police.
The warrants were issued shortly after protest leaders called an end to the stand-off.
Speaking to the BBC from hiding, protest leader Jakrapap Penkair called the retreat "an honourable decision to save lives", but vowed that the movement would continue.
Last week the protests forced the cancellation of an Asian summit, as crowds of demonstrators swarmed the summit venue.
Clashes then erupted in Bangkok, culminating in a day of violence on Monday that left more than 120 people injured.
Troops fought running battles with protesters, who hurled petrol bombs and drove commandeered buses at them. Soldiers responded with live rounds, something the armed forces' chief stressed was in self-defence.
PM Abhisit welcomed the end of the protests, but said that his government would remain on guard.
"The operation under the state of emergency is not over," he said. "There are still things to do. I insist the government will not be negligent because we have to remain vigilant."
Thailand remains deeply divided, with little consensus over who should govern, reports the BBC's Jonathan Head, from Bangkok.
Society is split between the urban and rural poor who support Mr Thaksin, and his foes in the traditional power cliques of the military and bureaucracy.
Mr Thaksin's allies won the election that followed the 2006 coup, but a court then ruled that the government was illegal, leaving Mr Abhisit - then the opposition leader - in a position to form a governing coalition.
The prime minister was helped into power by another group of protesters who shut down the main international airport for a week. None of those protesters have been detained or put on trial.
How Mr Abhisit deals with both groups of protesters will be seen by many here as a test of his pledge to uphold the law equally for all Thais, our correspondent says.