Molybdenum (Mo) is a commonly used material as the electrical back contact for Cu(In,Ga)Se-2 (CIGS) thin film solar cells taking advantages in electrical, structural and chemical properties. Bilayer structures have been actively examined to achieve Mo films of high conductivity with good substrate adhesion, which will also enable monolithically integrated solar cell modules on flexible platforms by combining laser scribing technology. However, reports on the bilayers on flexible substrates and their scribing by laser are very limited. In this study, we report the characteristics of bilayer Mo films deposited on a flexible polyimide substrate and the impact on the performance of picosecond laser scribing. Bilayer Mo films were deposited over a range of sputtering pressures and discharge powers as well as top-bottom layer thickness ratios, and laser scribing behavior was compared in the practical scribing speed range of the order of m/s. It is shown that microstructural and interfacial characteristics set by top and bottom Mo layers deposition parameters are critical factors influencing laser scribing quality.