Abstract We investigated the electrical transport characteristics of nanoscale stacks of thin graphite layer fabricated using focused ion beam (FIB) three dimensional (3D) etching. By varying the stack height, we fabricated nanostacks with the dimensions of W = 1 μm, L = 1 μm, H = 100 nm and W = 1 μm, L = 1 μm, H = 200 nm. The nanostack contains lot of elementary junctions between the graphene layers with interlayer distance of 0.34 nm (along c-axis). We observed a typical semiconducting characteristic until 50 K and a metallic behavior below 50 K for all the fabricated nanostacks, which was well agreed with an identical c-axis characteristics of graphite. From I–V characteristics, we found an ohmic-like characteristic at 300 K for both low and high current biasing; however at low temperature, this behavior was turned into nonlinear characteristics when it was highly biased. The temperature dependent differential conductance measurements for the fabricated stacks were carried out and found that at 300 K, the stack showed larger conductance rather than at any other lower temperatures. However, the stack with 100 nm height showed larger conduction values of 36.3 mS and 16.95 mS for 300 K and 20 K respectively, which are comparatively smaller values of stack with 200 nm height. We also studied conductance fluctuations of nanostacks experimentally and the fluctuations are appearing on increasingly fine when the temperature goes down; however the amplitude of fluctuation is suppressed at low temperature.