Defense attorney Deborah Colson indicated there was no plea deal in the works for the father of Najibullah Zazi, the admitted mastermind of the plot.
"We're definitely going to trial," Colson said outside federal court in Brooklyn after her client pleaded not guilty to witness tampering and lying to the FBI.
A judge set a July 11 date for potential jurors to start filling out questionnaires.
The 54-year-old Mohammed Wali Zazi, who lives in a Denver suburb, remains free on bail.
Najibullah Zazi is cooperating in an ongoing investigation of the plot and its roots in Pakistan, where Zazi said he went with former high school friends in 2008 to seek terror training from al-Qaida.
Zazi, a Colorado airport van driver, admitted that once back from Pakistan he tested peroxide-based explosive materials in a Denver suburb before traveling by car to New York intending to attack the subway system to avenge U.S. military involvement in Afghanistan.
Prosecutors say the two friends, Adis Medunjanin and Zarein Ahmedzay, agreed to join Zazi last year in what prosecutors described as "three coordinated suicide bombing attacks" on Manhattan subway lines. The would-be attacks were timed for days after the eighth anniversary of the Sept. 11 terror attacks.
The plot was disrupted in early September when police stopped Zazi's car as it entered New York.
FBI agents originally arrested Zazi's father on obstruction charges, alleging he conspired with others to destroy or hide "glasses, masks, liquid chemicals and containers" that were evidence in the case.
A new indictment filed last month added more obstruction counts, along with a charge alleging that the elder Zazi lied when he denied having a telephone conversation with a Queens imam about his son being in trouble. The indictment also alleges he supplied false information for an asylum application for his nephew.
Medunjanin is fighting terrorism charges. Ahmedzay has pleaded guilty.
Last week, lawyers for Medunjanin filed papers asking a judge to suppress statements he made after he was detained in January. He accused FBI agents of coercion, saying they made veiled threats against his family and denied him access to his attorney for 36 hours.
"You know what you've done," Medunjanin quoted one officer as saying. "If you want your family to be happy, you have to come with us."
Medunjanin said he knew Zazi's father had been arrested and feared if he didn't talk authorities "would find excuses to bring charges against members of my family."
The government has not responded to the defense motion. A hearing was set for Jan. 23.