The court has already declared the former military ruler an "absconder" in the Bhutto assassination case as he has not agreed to clarify his position in court despite several notices.
The Federal Investigation Agency (FIA) had requested the court to summon Musharraf, who was President at the time of the assassination, and has refused a request to cooperate in the investigation into Bhutto''s death.
Following the lack of cooperation by Musharraf, he was named an "absconding accused", FIA prosecutor Chaudhry Zulfiqar said.
The FIA today presented a final report in the court about Musharraf''s refusal to appear and the court issued orders to confiscate his property.
Local media reported that the court has also ordered freezing of Musharraf banks accounts.
The court ruled that the trial of Musharraf will be started separately from other accused and after he is arrested.
The anti-terrorism court is conducting the trial of five terror suspects, including alleged members of the Tehrik-e- Taliban Pakistan, who have been charged with planning and facilitating the assassination.
Bhutto was killed by a suicide bomber shortly after she addressed an election rally in Rawalpindi on December 27, 2007.