Federal courts are reserved for defendants accused of federal crimes. Investigations into alleged crimes are conducted by one or more U.S. government agencies, depending upon an agency's area of expertise. For example, the Internal Revenue Service may be involved in a white collar crime investigation specifically to address a tax fraud issue.
Federal agents may arrest a person with or without an arrest warrant. However, search warrants are used to gather evidence. Federal grand juries also issue subpoenas to compel anyone who might be helpful to the investigation to testify.
From this testimony, federal grand juries determine whether probable cause exists to charge and prosecute an individual. An arrest may precede or follow an indictment. The defendant hears the charges and is reminded of his or her rights during the first court appearance, which must happen within 72 hours of an arrest.
Formal charges are delivered during an arraignment, when a defendant is required to enter a plea. Provided that no guilty plea is entered, a discovery process takes place involving an exchange of materials and information between the defense and prosecutors. This is also a time when defense motions may be filed to challenge charges or evidence.
Many criminal cases are resolved through plea bargaining before any trial occurs. In a plea bargain, the defendant pleads guilty in exchange for a concession like a charge dismissal or a reduced sentence.
A federal judge may accept, reject or ask for modifications of a plea agreement. Rejections mean that defendants may choose to change pleas to not guilty, opening the way for the case to move to trial. It's always best to have the counsel of a criminal defense attorney who can advise you of the best option for your situation.
Source: The Federal Bureau of Investigation, "A Brief Description of the Federal Criminal Justice Process," accessed April. 28, 2015