Patituce said he didn't want to tip the defense strategy but said it would involve the CIA and a secretive operation decades ago in Arizona.
The judge indicated both sides had tried to resolve the case before trial, but, when questioned by the judge, Patituce said nothing had developed.
Thompson was dressed in a suit and tie and passed notes to his attorney during final motions. Jury selection began afterward.
Patituce said he needed more time to prepare and cited the 20,000 documents which must be reviewed. The judge said the trial would move ahead.
His attorney said any fraud involved solicitors, not his client.
Authorities said the defendant used his VIP political connections to encourage donors to give to his charity.
While on the run, investigators tracked him through Arizona, Florida, Indiana, Massachusetts, Rhode Island, Washington and West Virginia.