The Hubble Ultra Deep field (HUDF) is the deepest region ever observed with the Hubble Space Telescope. With the main objective of unveiling the nature of galaxies up to z~7-8, the observing and reduction strategy have focused on the properties of small and unresolved objects, rather than the outskirts of the largest objects, which are usually over-subtracted. We aim to create a new set of WFC3 IR mosaics of the HUDF using novel techniques to preserve the properties of the low surface brightness regions. We created ABYSS a pipeline that optimises the estimate and modelling of low-level systematic effects to obtain a robust background subtraction. We have improved four key points in the reduction: 1) creation of new absolute sky flat fields, 2) extended persistence models, 3) dedicated sky background subtraction and 4) robust co-adding. The new mosaics successfully recover the low surface brightness structure removed on the previous HUDF published reductions. The amount of light recovered with a mean surface brightness dimmer than mu=26mag/arcsec^2^ is equivalent to a m=19 mag source when compared to the XDF and a m=20mag compared to the HUDF12. We present a set of techniques to reduce ultra-deep images (mu>32.5mag/arcsec^2^, 3 sigma in 10x10 arcsec boxes), that successfully allow to detect the low surface brightness structure of extended sources on ultra deep surveys. The developed procedures are applicable to HST, JWST, EUCLID and many other space and ground-based observatories. We made the final ABYSS WFC3 IR HUDF mosaics publicly available at http://www.iac.es/proyecto/abyss/.