He had spent the night in detention at police headquarters in Islamabad and returned there after his court appearance.
Later in the afternoon, Musharraf was taken back to his farmhouse guarded by armed security personnel.
Live television footage showed Musharraf arriving at the heavily-guarded farmhouse.
Earlier yesterday, 69-year-old Musharraf was produced before Judge Kausar Abbas Zaidi of the anti-terrorism court amid chaotic scenes with lawyers raising slogans against the former President and scuffling with his supporters.
A grim-looking Musharraf walked the short distance from his SUV to the court, surrounded by his bodyguards and dozens of security personnel.
He waved and saluted to his followers before entering the courtroom on the first floor of the building. No one was allowed to come close to him. Musharraf waved to his followers again as he left the court.
The Judge remanded him to judicial custody till May 4, a day after his arrest for treason for detaining over 60 judges after declaring emergency in 2007.
A three-member Supreme Court bench has also been constituted to hear petitions seeking directions for initiating high treason trial against Musharraf for subverting the constitution and imposing emergency.
Zaidi briefly reserved his judgment before announcing his decision. He directed authorities to produce Musharraf in court again on May 4.
During the hearing held at the court complex in Sector F-8 in the heart of Islamabad, Musharraf's lawyer Qamar Afzal told the judge that he was cooperating with police officials investigating the detention of judges during emergency.
Afzal opposed any move to remand Musharraf to police custody, citing security concerns.
He further said Musharraf could approach the Supreme Court to appeal against the revocation of his bail by the Islamabad High Court.
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