Godden’s body was found in a shallow grave in a field in Eastleach, Gloucestershire, eight years after she disappeared.
Wiltshire police charged Halliwell, of Swindon, with her murder on 30 March.
The father of three appeared via videolink from Long Lartin prison in Worcestershire. He confirmed that he had decided to represent himself during the murder trial, which was scheduled to begin on 5 September before the retired high court judge Sir John Griffith Williams.
Mr Justice Openshaw told the court: “If he needs access to law books, everything should be done to ensure that he can properly prepare for his defence.”
Steps will be taken to ensure Halliwell can have his papers and a table in the dock, from where he will cross-examine witnesses.
Godden’s mother Karen Edwards, stepfather Charlie Edwards and father John Godden sat in the packed public gallery of the courtroom.
Nicholas Haggan QC, prosecuting, said 100 witnesses including nine experts could give evidence during the trial.
A further pre-trial hearing will take place before the end of July on a date to be fixed.
The judge remanded Halliwell in custody and told him: “Okay Mr Halliwell, I will now speak to the trial judge to suggest that he arranges a date towards the end of July and the case will be mentioned again for a series of further orders to be made.
“I have suggested to Mr Haggan that he produce a document setting out the 100 or so witnesses who presently are to give evidence against you, and setting out very briefly the nature of the evidence they are to give, and you should indicate whether you require them to attend in person.”
The last confirmed sighting of Godden before her remains were found in March 2011 was by a police officer in Swindon in December 2002.
She had drifted into drugs and prostitution, and her family thought was living in the Bristol area.
Godden had broken off contact with her family after saying she could not put her mother through the pain of watching her succumb to drugs.