A major challenge in the use of electrospun scaffolds for tissue generation is that tightly packed layers of nanofibers can block cell infiltration into the scaffold, resulting in non-homogeneous cell distribution. This can cause incomplete extracellular matrix deposition and failure to generate tissue. In this study, we developed a cell seeding method that supports cell infiltration and distribution within a three-dimensional (3D) flexible and shape-controllable electropun scaffold. Cells were seeded on the scaffold layer-by-layer and cell growth rate 7 days post seeding was compared to cell growth after traditional cell seeding. Scanning electron microscopy demonstrated that the shape-controlled scaffold consist of microfibers with uniform thickness. In using the layer-by-layer seeding method, we observed that the cells were distributed uniformly throughout the 3D scaffold. In contrast, use of the traditional cell seeding method resulted in the cells remaining on the surface of the scaffold. These results suggest that a layer-by-layer cell seeding method can improve cell distribution within a 3D scaffold and effectively facilitate tissue formation.