There is an enormous variety of pretrial motions in a federal case. These can include motions to dismiss charges or suppress evidence, constitutional challenges, motions for a bill of particulars, motions to strike and motions in limine, and severance motions. See generally Fed. R. Crim. Pro. 12.
The most typical pretrial motion is a suppression motion. In these types of motions, the defense moves to suppress evidence, or to prevent the government from using it at trial. These motions can include suppression of evidence, like a gun or drugs seized in a search, or statements, like a defendant's confession.
The defendant's motion outlines the facts and law in support of the claim for relief. The prosecutor usually has about ten days to respond to that motion, and the defense has a right to a final written reply. Sometime thereafter, the magistrate hears argument on the motion and takes witness testimony if needed. This is called an evidentiary hearing to resolve any disputed facts. The magistrate will then file a "Report and Recommendation" with the district judge. The district judge will give the parties ten days to file objections to this report, and later decide whether to accept or reject the magistrate's findings.