All five High Courts nominated a judge each and forwarded their names to the Supreme Court Registrar.
Chief Justice Iftikhar Chaudhry will now choose the three judges who will hear the treason case against Musharraf, a charge that could entail the death penalty or life imprisonment.
Also Read
The move to form the special court came after the Law Ministry asked the apex court to try the 70-year-old former army chief for high treason.
This is the first time the civilian administration has sought the criminal prosecution of a military ruler.
Musharraf's spokesperson has described the government's decision as a "vicious attempt to undermine the Pakistan military".
The military has ruled Pakistan for about half of its 66-year history and no ruler or top military commander has ever faced criminal prosecution.
Since Musharraf returned to Pakistan from self-exile in March, he has faced prosecution in four major cases, including one over the assassination of former Prime Minister Benazir Bhutto.
Interior Minister Chaudhry Nisar Ali Khan yesterday said the government decided to initiate treason proceedings against Musharraf under Article 6 of the Constitution in line with a judgement of the Supreme Court and a report submitted by an inquiry committee.
Information Minister Pervaiz Rashid had earlier in the day said that had the government not initiated the treason trial against Musharraf, the former dictator would have been "sitting abroad".