Monolithic three-dimensional integrated circuits (M3D ICs) are being advocated as the next generation of 3D integration beyond 3D ICs based on through-silicon-vias. Testing of the bottom layer of an M3D IC is necessary to target defects arising from the layered manufacturing process. We present an efficient design-for-test (DfT) method for the bottom layer by isolating it from the top layer. A bypass structure based on e-fuses is proposed to connect pairs of inter-layer vias (ILVs). In order to minimize the wire length between paired ILVs, an ILV-pairing problem is formulated and then solved using a technique based on maximum-weighted bipartite matching. The independent ILVs, i.e., those that are not paired, are made controllable and observable using four different types of DfT structures. A cost-optimization problem is solved to minimize the DfT cost. We present ILV-pairing and cost-optimization results for designs based on the ITC′02 benchmarks as well as for an industry design. We also present HSpice simulation results to show that testing using e-fuses is feasible.