The resistance in series model has been frequently used for determination of various filtration resistance to correctly understand the membrane fouling behaviour in MBR (membrane bio-reactor) for wastewater treatment. The cake layer resistance (Rc) which is commonly determined by calculation of flux dataset that are obtained empirically before and after removing the cake layer on membrane surface. However, the calculated Rc values are very dependent on the cleaning methods adapted for removal of cake layer. This study investigated how the various cleaning options affect Rc. Seven different cleaning methods were employed: i) ultrasonication (100 W, 10 min), ii) ultrasonication (200 W, 60 min), iii) ultrasonication (400 W, 120 min), iv) water rinsing in a shaker (100 rpm, 10 min), v) water rinsing in a shaker (300 rpm, 60 min), vi) water rinsing, vii) sponge scrubbing. For the hydrophilic PES membrane, the cake layer removal efficiencies ranged from 64% to 10%, indicating that the removal of cake layer was highly dependent on the cleaning options. For the hydrophobic PVDF membrane, the cake layer removal efficiencies ranged from 79% to 97%. Consequently, a standardized method for cake layer removal to determine cake resistance (Rc) is needed for correct interpretation of the fouling phenomena.