The MUSE processed data cubes downloaded from the ESO Science Archive Facility (see announcement) are sky subtracted but may still include residuals of sky emission lines redward of λ > 7000Å. These residuals can be further reduced using a dedicated ESO Reflex interactive workflow, to be applied directly to the MUSE science data products.
Removal of Sky Residuals from MUSE Data Cubes
The Reflex interactive workflow, called muse_zap, uses the Zurich Atmosphere Purge code (ZAP, Soto et al. 2016, MNRAS, 458, 3210) and is available, together with the MUSE pipeline and other workflows, from the ESO Instrument Pipelines webpage.
A tutorial, plus detailed instructions on the installation procedure and usage of the workflow, are also available here.