We investigate the topological properties of spin polarized fermionic polar molecules loaded in a multi-layer structure with the electric dipole moment polarized to the normal direction. When polar molecules are paired by attractive inter-layer interaction, unpaired Majorana fermions can be macroscopically generated in the top and bottom layers in dilute density regime. We show that the resulting topological state is effectively composed by a bundle of 1D Kitaev ladders labeled by in-plane momenta k and -k, and hence belongs to BDI class characterized by the winding number Z, protected by the time reversal symmetry. The Majorana surface modes exhibit a flatband at zero energy, fully gapped from Bogoliubov excitations in the bulk, and hence becomes an idea system to investigate the interaction effects on quantum degenerate Majorana fermions. We further show that additional interference fringes can be identified as a signature of such 2D Majorana surface modes in the time-of-flight experiment.