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With the advent of modern multidetector heterodyne instruments that can result in observations generating thousands of spectra per minute it is no longer feasible to reduce these data as individual spectra. We describe the automated data reduction procedure used to generate baselined data cubes from heterodyne data obtained at the James Clerk Maxwell Telescope (JCMT). The system can automatically detect baseline regions in spectra and automatically determine regridding parameters, all without input from a user. Additionally, it can detect and remove spectra suffering from transient interference effects or anomalous baselines. The pipeline is written as a set of recipes using the ORAC-DR pipeline environment with the algorithmic code using Starlink software packages and infrastructure. The algorithms presented here can be applied to other heterodyne array instruments and have been applied to data from historical J C M T heterodyne instrumentation. [ABSTRACT FROM AUTHOR]