For successful skeletal muscle tissue regeneration, inducing alignment and fusion of myoblasts into multinucleated myotubes is critical. Many studies are ongoing to induce myoblast alignment using various micro/nanopatternings on scaffold surfaces, mechanically stretching scaffolds, or aligned micro/nanofibers. In this study, we have developed a simple method to induce myoblast alignment using a modified plasma treatment on a hybrid PCL scaffold consisting of melt-printed perpendicular PCL struts and an electrospun PCL fibrous mat. For the hybrid scaffold, the surface of the electrospun mat was selectively roughened with a plasma process supplemented with a template. The cell alignment of myoblasts using this system was enhanced significantly when compared to results from the use of a hybrid scaffold with a non-roughened electrospun fiber surface or a hybrid scaffold where the whole surface of the electrospun fibers was roughened. This new type of plasma-treated hybrid scaffold has strong potential as a biomaterial for use in muscle tissue regeneration.