This paper presents a novel approach to fault tolerant reconfiguration of modular self-folding robots. Among various types of faults that probably occur in the modular system, we focus on the tolerance of complete actuation failure of active modules that might cause imprecise robotic motion and even reconfiguration failure. Our approach is to utilize the reconfigurability of modular self-folding robots and investigate intra-module connection to determine initial patterns that are inherently fault tolerant. We exploit the redundancy of actuation and distribute active modules in both layout-based and target-based scenarios, such that reconfiguration schemes with user-specified fault tolerant capability can be generated for an arbitrary input initial pattern or 3D configuration. Our methods are demonstrated in computer-aided simulation on the robotic platform of Mori, a modular origami robot. The simulation results validate that the proposed algorithms yield fault tolerant initial patterns and distribution schemes of active modules for several 2D and 3D configurations with Mori, while retaining generalizability for a large number of modular self-folding robots.