Hybrid PET/MR offers new opportunities in radiation oncology for tissue/tumour characterisation and response assessment. Attenuation correction (AC) is an important issue especially in the presence of immobilization devices and flat table tops (FTT). The goal of this study was to compare two methods of AC using CT- and Ge/Ga transmission scan-based attenuation maps (μ-maps) for a custom-designed FTT. Measurements were performed in the mMR PET/MR and TrueV PET/CT Biograph Siemens scanners with three different phantoms, namely the Siemens MR-QA, a cubic canister and the NEMA IEC body phantom. The study revealed that the MR image quality is not hampered by the presence of the FTT. For cubic canister applying the scanner's inherent AC alone resulted in inaccuracies in PET images, with up to -4.0% underestimation of the activity. The mean NEMA sphere activity measurements without FTT, agreed within 3.5% with the respective inserted activity. Placing the FTT in the PET/MR scanner resulted in a difference to the injected activity of 4.5% when the table was not corrected for. By introducing the μ-maps the discrepancy between the used activity and the measurements decreased down to 2.6%. To improve the AC of the FTT the creation of a dedicated μ-map was necessary while the CT-based μ-map performed equally good as the source transmission scan-based one.