<jats:title>Abstract</jats:title> <jats:p>The Molecules with ALMA at Planet-forming Scales Large Program (MAPS LP) surveyed the chemical structures of five protoplanetary disks across more than 40 different spectral lines at high angular resolution (0.″15 and 0.″30 beams for Bands 6 and 3, respectively) and sensitivity (spanning 0.3–1.3 mJy beam<jats:sup>−1</jats:sup> and 0.4–1.9 mJy beam<jats:sup>−1</jats:sup> for Bands 6 and 3, respectively). In this article, we describe the multistage workflow—built around the CASA <jats:monospace>tclean</jats:monospace> image deconvolution procedure—that we used to generate the core data product of the MAPS LP: the position–position–velocity image cubes for each spectral line. Owing to the expansive nature of the survey, we encountered a range of imaging challenges: some are familiar to the submillimeter protoplanetary disk community, like the need to use an accurate CLEAN mask, and others are less well known, like the incorrect default flux scaling of the CLEAN residual map first described by Jorsater & van Moorsel (the “JvM effect”). We distill lessons learned into recommended workflows for synthesizing image cubes of molecular emission. In particular, we describe how to produce image cubes with accurate fluxes via “JvM correction,” a procedure that is generally applicable to any image synthesized via CLEAN deconvolution but is especially critical for low signal-to-noise ratio (S/N) emission. We further explain how we used visibility tapering to promote a common, fiducial beam size and contextualize the interpretation of S/N when detecting molecular emission from protoplanetary disks. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement.</jats:p>