The indictment should be dismissed because it is impermissibly vague, would confuse jurors and presented the risk that Clemens would be wrongly convicted, his lawyers argued in a 13-page filing.
Clemens, 48, who won the Cy Young Award seven times as his league's best pitcher, has pleaded not guilty to three counts of making false statements, two counts of perjury and one count of obstructing the U.S. Congress.
His trial is scheduled to start in July.
The charges stemmed from the denial by Clemens under oath in 2008 of using steroids and human growth hormone to the staff of the House of Representatives' Committee on Oversight and Government Reform and again during a congressional hearing.
His lawyers argued that one of the key counts in the indictment was impermissibly duplicative and that Clemens had not been adequately informed of the true nature of the accusations against him.
Even Roger Clemens cannot pitch a shutout if nobody knows the boundaries of the strike zone, they wrote in the court filing. The indictment should ... be dismissed in its entirety.
Federal prosecutors said they planned to offer evidence during the trial that included records from cell phone providers, banks, baseball teams he played for, including the Boston Red Sox and New York Yankees, and even social media websites like Twitter.
After his indictment, Clemens asserted his innocence on Twitter, denying he took human growth hormone or steroids and denying he lied to Congress.