Since its launch in 1999, the Far Ultraviolet Spectroscopic Explorer (FUSE) has made over 4900 observations of some 2500 individual targets. The data are reduced by the principal investigator team at the Johns Hopkins University and archived at the Multimission Archive at STScI (MAST). The data reduction software package, called CalFUSE, has evolved considerably over the lifetime of the mission. The entire FUSE data set has recently been reprocessed with CalFUSE version 3.2, the latest version of this software. This paper describes CalFUSE version 3.2, the instrument calibrations on which it is based, and the format of the resulting calibrated data files.